Indirect homogeneous mobility shift assays for the detection of biologics in patient samples

ABSTRACT

The present invention provides a sensitive and specific indirect homogeneous mobility shift assay using size exclusion chromatography to measure biologics such as vedolizumab and ustekinumab in a patient sample. The assays of the present invention are particularly advantageous for detecting the presence or level of biologics that target complex or large antigens including cell surface proteins, transmembrane proteins, heavily glycosylated proteins, and multimeric proteins, as well as antigens that cannot be purified, impure antigens, and partially or substantially purified antigens. The present invention also provides isolated soluble α4β7 integrin heterodimers and isolated soluble IL-12p40 monomers that are suitable for use in the indirect assays described herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/603,137 filed May 23, 2017 which is a continuation ofPCT/IB2015/059381, filed Dec. 4, 2015, which claims priority to U.S.Provisional Application No. 62/088,465, filed Dec. 5, 2014, U.S.Provisional Application No. 62/113,317, filed Feb. 6, 2015, and U.S.Provisional Application No. 62/158,791, filed May 8, 2015, thedisclosures of which are hereby incorporated by reference in theirentirety for all purposes.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 8, 2019 isnamed 56884867302 SL.txt and is 40,507 bytes in size.

BACKGROUND OF THE INVENTION

Inflammatory bowel disease (IBD), which occurs world-wide and afflictsmillions of people, is the collective term used to describe threegastrointestinal disorders of unknown etiology: Crohn's disease (CD),ulcerative colitis (UC), and indeterminate colitis (IC). IBD, togetherwith irritable bowel syndrome (IBS), will affect one-half of allAmericans during their lifetime, at a cost of greater than $2.6 billiondollars for IBD and greater than $8 billion dollars for IBS. A primarydeterminant of these high medical costs is the difficulty of diagnosingdigestive diseases and how these diseases will progress. The cost of IBDand IBS is compounded by lost productivity, with people suffering fromthese disorders missing at least 8 more days of work annually than thenational average.

Despite the successes of anti-TNFα therapies in the treatment of IBD, asubpopulation of patients are refractory to treatment, highlighting anunmet medical need for new therapies. Vedolizumab is a gut-specific,α4β7 integrin-neutralizing monoclonal antibody, which does not affectperipheral blood cell counts and appears to lack systemic effects.Vedolizumab is a new anti-inflammatory treatment option for themanagement of therapy-refractory patients. In addition, ustekinumab is aIL12p40 monoclonal antibody, which is another novel IBD therapeutic.However, the availability of diagnostic tests to accurately measure thelevels of biologics such as vedolizumab and ustekinumab is necessary forthe effective use of these novel therapeutics in IBD patients.

As such, there is a need in the art for assays to detect the presence orlevel of biologics such as vedolizumab and ustekinumab in a patientsample to monitor drug therapy and to guide treatment decisions. Suchassays are particularly useful for the therapeutic management ofdiseases such as ulcerative colitis and Crohn's disease using anindividualized approach to monitor drug efficacy and optimize therapyaccordingly, and can include assessing disease course and clinicalparameters such as pharmacodynamics, disease activity indices, diseaseburden, and inflammatory biomarkers. The present invention satisfiesthis need and provides related advantages as well.

BRIEF SUMMARY OF THE INVENTION

The present invention provides novel indirect homogeneous mobility shiftassays for detecting and measuring the presence or level of a biologicin a sample. The assays of the present invention are particularlyadvantageous for detecting and measuring the presence or level ofbiologics that target complex antigens including cell surface proteins,transmembrane proteins, heavily glycosylated proteins, multimericproteins, and the like. As such, the present invention providesinformation for guiding treatment decisions for those subjects receivingtherapy with a biologic agent and improves the accuracy of optimizingtherapy, reducing toxicity, and/or monitoring the efficacy oftherapeutic treatment to biologic therapy. The present invention alsoprovides isolated soluble α4β7 integrin heterodimers and isolatedsoluble IL-12p40 monomers that are suitable for use in the assaysdescribed herein.

In certain aspects, the present invention provides a method fordetermining the presence or level of a biologic in a sample, the methodcomprising:

-   -   (a) contacting the sample with an unlabeled soluble antigen that        binds to the biologic to form an unlabeled complex between the        antigen and the biologic in the sample;    -   (b) contacting the sample from step (a) with a labeled form of        the biologic to form a labeled complex between the antigen and        the labeled biologic;    -   (c) subjecting the unlabeled and labeled complexes to size        exclusion chromatography to separate the unlabeled and labeled        complexes from free labeled biologic and to detect an amount of        the free labeled biologic; and    -   (d) comparing the amount of the free labeled biologic detected        in step (c) to a standard curve of known amounts of the        biologic, thereby determining the presence or level of the        biologic in the sample.

In some embodiments, the biologic includes antibodies, antibodyfragments, proteins, polypeptides, peptides, fusion proteins,multivalent binding proteins, antibody-drug conjugates, vaccines,nucleic acids, sugars, recombinant forms thereof, engineered formsthereof, and combinations thereof.

In certain embodiments, the antigen is a soluble version (e.g., asoluble fragment, variant, or monomeric form) of a membrane-boundprotein, a glycosylated protein, a multimeric protein, an insolubleprotein, a protein that is difficult to express or purify, and/or alarge protein. In certain instances, the antigen is a solubleextracellular domain of a membrane-bound protein (e.g., a solublecytokine receptor extracellular domain). In certain other instances, theantigen is a soluble homodimer or heterodimer comprising theextracellular domains of two membrane-bound proteins (e.g., a solubleintegrin heterodimer). In yet other instances, the antigen is a solubleprotein that does not multimerize and remains in monomeric form onceisolated and/or purified (e.g., a soluble cytokine variant with one ormore cysteine residues mutated to minimize or eliminate the formation ofmultimers).

In other embodiments, the sample is a whole blood, serum, or plasmasample, e.g., from a subject receiving biologic therapy. In preferredembodiments, the sample is serum. In particular embodiments, the subjecthas a disease or disorder such as, e.g., an autoimmune disease (e.g.,rheumatoid arthritis), an inflammatory disease (e.g., inflammatory boweldisease (IBD) such as Crohn's disease (CD) or ulcerative colitis (UC)),or cancer.

In particular embodiments, the standard curve is generated by incubatingthe antigen and the labeled biologic with a (e.g., two-fold) serialdilution of known amounts of the biologic. In certain embodiments, thearea under the curve (AUC) of the free labeled biologic is plottedagainst (e.g., the logarithm of) known amounts of the biologic obtainedfrom the standard curve, and the level of the biologic in the sample iscalculated by interpolation, e.g., based upon the size of the peak areaof the free labeled biologic. In other embodiments, free label added toa stock solution of labeled biologic is used as a labeled biologicloading control. The ratio of the free labeled biologic to free label isplotted against known amounts of biologic.

In one particular embodiment, the presence and/or level of an anti-α4β7integrin drug (e.g., vedolizumab) is determined with an indirecthomogeneous mobility shift assay using size exclusion chromatography asdescribed herein.

In another particular embodiment, the presence and/or level of ananti-IL12p40 drug (e.g., ustekinumab) is determined with an indirecthomogeneous mobility shift assay using size exclusion chromatography asdescribed herein.

In other embodiments, the presence and/or level of anti-drug antibodies(ADA) (e.g., autoantibodies including HACA, HAHA, etc.) that aregenerated against anti-α4β7 integrin drugs and anti-IL12p40 drugs aswell as other biologics is determined with a homogeneous mobility shiftassay as described in, e.g., U.S. Pat. Nos. 8,574,855 and 8,865,417, andU.S. Patent Publication Nos. 2014/0051184 and 2014/0141983, thedisclosures of which are hereby incorporated by reference in theirentirety for all purposes.

In other aspects, the present invention provides an isolated soluble α4integrin polypeptide comprising an amino acid sequence having at least80% identity to SEQ ID NO:1 or SEQ ID NO:3. In yet other aspects, thepresent invention provides an isolated soluble (37 integrin polypeptidecomprising an amino acid sequence having at least 80% identity to SEQ IDNO: 2 or SEQ ID NO:4.

In particular embodiments, the present invention provides an isolatedsoluble α4β7 integrin heterodimer comprising:

-   -   (a) an α4 integrin polypeptide having an amino acid sequence        that has at least 80% identity to SEQ ID NO:1, wherein the α4        integrin polypeptide is linked to a first member of a binding        pair (e.g., SEQ ID NO:3), and    -   (b) a β7 integrin polypeptide having an amino acid sequence that        has at least 80% identity to SEQ ID NO:2, wherein the β7        integrin polypeptide is linked to a second member of the binding        pair (e.g., SEQ ID NO:4).

In certain other aspects, the present invention provides an isolatedsoluble IL-12p40 polypeptide comprising an amino acid sequence having atleast 80% identity to SEQ ID NOS:6, 7, 11, 12, or 13.

In particular embodiments, the unlabeled soluble antigen used in theindirect homogeneous mobility shift assays of the present inventioncomprise the isolated soluble α4β7 integrin heterodimers or isolatedsoluble IL-12p40 polypeptides described herein.

In further aspects, the present invention provides expression vectorsencoding the soluble polypeptides described herein, host cellscomprising the expression vectors, and methods for generating thesoluble polypeptides described herein.

Other objects, features, and advantages of the present invention will beapparent to one of skill in the art from the following detaileddescription and figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the principle of the indirect homogeneous mobility shiftassays (HMSA) of the present invention. Using vedolizumab (“VLM” or“Vedo”) as a non-limiting example, in the first step, serum is added toa 96 well plate along with integrin α4β7 and diluent buffer. In thesecond step, labeled VLM (e.g., Vedo Alexa 488) is added. The samplesare then injected sequentially on an HPLC size exclusion column.

FIG. 2 shows the chromatograms of Vedo Alexa 488 (left) and Vedo Alexa488 plus integrin α4β7 antigen (right) with retention times (x-axis) andlight units (y-axis) of one embodiment of the present invention. Bothare in 4% normal human serum. Note that the antigen binds up themajority of the labeled VLM.

FIG. 3 shows the chromatograms from standard curve overlays with theretention time (x-axis) and light units (y-axis) of the variouscomponents of a VLM assay in one embodiment of the present invention.“Vedo Alexa 488/α4β7”=Alexa Fluor® 488-labeled VLM bound to a solubleα4β7 heterodimer. “Alexa 488”=Blocked (e.g., inactivated) Alexa Fluor®488 loading control.” Note that the free Vedo Alexa 488 peak area getslarger when there is more therapeutic VLM present.

FIG. 4 shows a VLM standard curve in one embodiment of the presentinvention. The standard curve was generated using a serial dilution ofVLM with a concentration range of between 0.15625 μg/ml and 80 μg/ml.

FIG. 5 shows a VLM drug assay validation in one embodiment of thepresent invention. The limit of blank (LOB), limit of detection (LOD),lower limit of quantitation (LLOQ), and upper limit of quantitation(ULOQ) were calculated using a standard curve generated from a serialdilution of VLM with a concentration range of between 0.15625 μg/ml and80 μg/ml.

FIG. 6 shows the intra-assay precision and accuracy of the VLM drugassay in one embodiment of the present invention.

FIG. 7 shows the retention time (x-axis) and light units (y-axis) of ananti-vedolizumab autoantibody (ATV) assay in one embodiment of thepresent invention.

FIG. 8 shows the validation of the ATV assay in one embodiment of thepresent invention.

FIG. 9 shows the validation of the ATV assay in one embodiment of thepresent invention.

FIG. 10 shows the interassay precision of the ATV assay in oneembodiment of the present invention.

FIG. 11 shows a ustekinumab (UTK) drug assay validation in oneembodiment of the present invention. The limit of blank (LOB), limit ofdetection (LOD), lower limit of quantitation (LLOQ), and upper limit ofquantitation (ULOQ) were calculated using a standard curve generatedfrom a serial dilution of UTK with a concentration range of between0.078 μg/ml and 40 μg/ml.

FIG. 12 shows the validation of the assay for autoantibodies toustekinumab (ATU) in one embodiment of the present invention.

FIG. 13 shows a schematic diagram of the exemplary embodiments of thesoluble α4 integrin antigen and soluble β7 integrin antigen of thepresent invention. Left: Full-length proteins. Right: Truncated α4β7integrin heterodimer with a cysteine bridge of the ACID-BASE peptide.

FIGS. 14A and 14B show the linearity of drug dilution in human serum for(A) VLM and (B) autoantibodies to vedolizumab (ATV).

FIGS. 15A, 15B and 15C show an analysis of common interfering agents inserum: (A) hemolyzed serum interference; (B) lipemic serum interference;and (C) RF serum interference.

FIG. 16 shows the principle of the ustekinumab (UTK) homogeneousmobility shift assay (HMSA).

FIGS. 17A and 17B show the linearity of dilution in normal human serumfor (A) UTK and (B) autoantibodies to ustekinumab (ATU).

FIGS. 18A, 18B and 18C show an analysis of common interfering agents inserum: (A) hemolyzed serum interference; (B) lipemic serum interference;and (C) RF serum interference.

FIG. 19 shows integrin α4β7 substrate interference in one embodiment ofthe VLM assay of the present invention.

FIG. 20 shows standard curves using fixed amounts of labeled vedolizumab(“Vedo488”) and integrin α4β7 antigen (top left), as well as 2-foldincreased (top right) or 4-fold increased (bottom left) amounts of bothreagents. Note that the top end of the curve saturates at higher VLMconcentrations. Similarly, the bottom end flattens out at slightlyhigher levels of VLM.

DETAILED DESCRIPTION OF THE INVENTION I. Introduction

The present invention is based in part on the discovery that an indirecthomogeneous mobility shift assay (HMSA) using size exclusionchromatography is particularly advantageous for measuring the presenceor level of biologics that target antigens having one or more of thefollowing characteristics: cell surface or membrane-bound, (heavily)glycosylated, multimeric (e.g., forms heterodimers, homodimers, etc.),insoluble, difficult to express, difficult to purify, large in size, andcombinations thereof. In certain aspects, the use of a soluble form(e.g., a soluble fragment, variant, or monomer) of the antigen overcomesthe difficulties and limitations associated with antigens having one ormore of the above characteristics and enables the precise and accuratemeasurement of any biologic of interest in a sample from a patientreceiving therapy with that biologic.

The principle behind the indirect assays of the present invention isthat the amount of (unlabeled) biologic in a sample (e.g., serum)obtained from a patient receiving biologic therapy determines how muchunlabeled antigen remains free to bind to a labeled form of thebiologic. By tracking changes in the area of the free (unbound) labeledbiologic, the presence or level of (unlabeled) biologic in the patientsample can be determined. More particularly, the relative amount (e.g.,ratio) of labeled and unlabeled biologic determines how much antigen isbound to each and determines the amount (e.g., peak area) of freelabeled biologic following size exclusion chromatography. The amount(e.g., peak area) of the free labeled biologic can then be compared to astandard curve of known amounts of the biologic to provide an accuratemeasurement of biologic levels in the patient sample with highsensitivity and dynamic range. In certain embodiments, the size of thepeak area of free labeled biologic following size exclusionchromatography is calculated and compared to the standard curve tointerpolate the concentration of biologic in a patient sample.

The importance of measuring serum concentrations of biologics isillustrated by the fact that the FDA requires pharmacokinetic andtolerability (e.g., immune response) studies to be performed duringclinical trials. The present invention also finds utility in monitoringpatients receiving these drugs to make sure they are getting the rightdose, that the drug isn't being cleared from the body too quickly, andthat they are not developing an immune response against the drug.Furthermore, the present invention is useful in guiding the switchbetween different drugs due to failure with the initial drug.

II. Definitions

As used herein, the following terms have the meanings ascribed to themunless specified otherwise.

The terms “a,” “an,” or “the” as used herein not only include aspectswith one member, but also include aspects with more than one member. Forinstance, the singular forms “a,” “an,” and “the” include pluralreferents unless the context clearly dictates otherwise.

The terms “competition,” “competition-based,” and “indirect” are usedinterchangeably herein to refer to an assay of the present invention fordetermining the presence or level of (unlabeled) biologic in a samplethat relies on detecting the amount of free (unbound) labeled biologicremaining in the sample after unlabeled antigen and labeled biologic areadded (sequentially) to the sample.

The terms “VLM,” “VDZ,” and “Vedo” are used interchangeably herein torefer to vedolizumab.

The terms “biologic” or “biologic agent” or “biological drug” as usedherein encompass products and substances produced from or extracted froma biological system (e.g., a living organism). Non-limiting examples ofbiologics include antibodies, antibody fragments, proteins,polypeptides, peptides, fusion proteins (e.g., Ig fusion proteins or Fcfusion proteins), multivalent binding proteins (e.g., DVD Ig),antibody-drug conjugates, vaccines, nucleic acids, sugars, recombinantforms thereof, engineered forms thereof, and combinations thereof.

The term “antibody” includes large (150 kDa) “Y-shaped” molecules thatconsist of two identical light chains (˜220 amino acids) and twoidentical heavy chains (˜440 amino acids) that are held together by acombination of covalent (disulfide) and non-covalent interactions. Eachlight and heavy chain consists of repeating segments of constant orvariable regions that contain one intrachain disulfide bond. Thevariable regions are located at the N-termini of the light and heavychains, while the constant domains are located at the C-termini of thelight and heavy chains. The N-termini of the light and heavy chains cometogether to form the antigen-binding site. The light chain is comprisedof one variable domain and one constant domain and the heavy chain iscomprised of one variable domain and three constant domains. Located atthe ends of the “Y” are two identical (bivalent) antigen-binding sites.The distance between the two antigen binding sites varies due to theflexible hinge region, and as a result, the antigen binding efficiencycan be greatly increased. The formation of the antigen-binding region iscaused by the pairing of the variable region from the heavy chain(V_(H)) with the variable region of the light chain (V_(L)). Variationsin amino acid sequences of the variable regions are responsible for thevast diversity of antigen-binding sites, and the greatest variabilityoccurs throughout three hypervariable regions, termed complementarydetermining regions (CDRs). The tail region of the antibody, known asthe F_(C) region, is comprised of two constant domains (C_(H)2, andC_(H)3) from each of the heavy chains. The F_(C) region is responsiblefor recruiting effector functions through binding of F_(C) receptors onneutrophils and macrophages.

The term “antigen” includes any molecule, agent, or substance that(e.g., specifically) binds to or interacts with a biologic. As onenon-limiting example, the antigen comprises a soluble fragment, variant,or monomer of a membrane-bound protein, a glycosylated protein, amultimeric protein, an insoluble protein, a protein that is difficult toexpress or purify, and/or a large protein. As another non-limitingexample, the antigen comprises a soluble fragment of a cell surfacemolecule such an integrin receptor (e.g., α4β7 integrin), wherein thesoluble fragment contains one or more extracellular domains of thecorresponding full-length molecule (e.g., a soluble α4β7 antigenheterodimer comprising extracellular domain sequences from thecorresponding full-length α4 and β7 proteins). As yet anothernon-limiting example, the antigen comprises a cytokine such as TNFα or asubunit thereof such as IL-12p40 that does not form homodimers orheterodimers.

The term “size exclusion chromatography” or “SEC” includes achromatographic method in which molecules in solution are separatedbased on their size and/or hydrodynamic volume. It is applied to largemolecules or macromolecular complexes such as proteins and theirconjugates. Typically, when an aqueous solution is used to transport thesample through the column, the technique is known as gel filtrationchromatography.

The term “complex” includes an antigen bound (e.g., by non-covalentmeans) to a biologic (e.g., an unlabeled or labeled biologic), and abiologic (e.g., a labeled biologic) bound (e.g., by non-covalent means)to an autoantibody against the biologic.

As used herein, an entity that is modified by the term “labeled”includes any antigen, molecule, protein, enzyme, antibody, antibodyfragment, cytokine, or related species that is conjugated with anothermolecule or chemical entity that is empirically detectable. Chemicalspecies suitable as labels include, but are not limited to, fluorescentdyes, e.g. Alexa Fluor® dyes such as Alexa Fluor® 488, quantum dots,optical dyes, luminescent dyes, and radionuclides, e.g., ¹²⁵I.

The phrase “fluorescence label detection” includes a means for detectinga fluorescent label. Means for detection include, but are not limitedto, a spectrometer, a fluorimeter, a photometer, and a detection devicecommonly incorporated with a chromatography instrument such as, but notlimited to, size exclusion-high performance liquid chromatography, suchas, but not limited to, an Agilent-1200 HPLC System.

The term “subject,” “patient,” or “individual” typically includeshumans, but also includes other animals such as, e.g., other primates,rodents, canines, felines, equines, ovines, porcines, and the like.

The term “sample” includes any biological specimen obtained from anindividual. Samples include, without limitation, whole blood, plasma,serum, red blood cells, white blood cells (e.g., peripheral bloodmononuclear cells (PBMC), polymorphonuclear (PMN) cells), ductal lavagefluid, nipple aspirate, lymph (e.g., disseminated tumor cells of thelymph node), bone marrow aspirate, saliva, urine, stool (i.e., feces),sputum, bronchial lavage fluid, tears, fine needle aspirate (e.g.,harvested by random periareolar fine needle aspiration), any otherbodily fluid, a tissue sample such as a biopsy of a site of inflammation(e.g., needle biopsy), cellular extracts thereof, and an immunoglobulinenriched fraction derived from one or more of these bodily fluids ortissues. In some embodiments, the sample is whole blood, a fractionalcomponent thereof such as plasma, serum, or a cell pellet, or animmunoglobulin enriched fraction thereof. One skilled in the art willappreciate that samples such as serum samples can be diluted prior tothe analysis. In certain embodiments, the sample is obtained byisolating PBMCs and/or PMN cells using any technique known in the art.In certain other embodiments, the sample is a tissue biopsy such as,e.g., from a site of inflammation such as a portion of thegastrointestinal tract or synovial tissue.

The term “isolated,” when applied to a nucleic acid or polypeptide,denotes that the nucleic acid or polypeptide is essentially free ofother cellular components with which it is associated in the naturalstate. It is preferably in a homogeneous state although it can be ineither a dry or aqueous solution. Purity and homogeneity are typicallydetermined using analytical chemistry techniques such as polyacrylamidegel electrophoresis or high performance liquid chromatography. Apolypeptide that is the predominant species present in a preparation issubstantially purified. In particular, an isolated gene is separatedfrom open reading frames that flank the gene and encode a protein otherthan the gene of interest. The term “purified” denotes that a nucleicacid or polypeptide gives rise to essentially one band in anelectrophoretic gel. Particularly, it means that the nucleic acid orpolypeptide is at least about 80% pure, at least about 85% pure, atleast about 90% pure, at least about 95% pure, or at least about 99%pure.

The term “soluble,” in the context of a polypeptide, refers topolypeptide that can be prepared in a soluble and functional form usinga host cell or a cell-free protein synthesis system. For instance, asoluble polypeptide does not form insoluble aggregates comprisingmisfolded and/or functionally inactive polypeptides.

The term “nucleic acid” or “polynucleotide” includesdeoxyribonucleotides or ribonucleotides and polymers thereof in eithersingle- or double-stranded form. Unless specifically limited, the termencompasses nucleic acids containing known analogues of naturalnucleotides that have similar binding properties as the referencenucleic acid and are metabolized in a manner similar to naturallyoccurring nucleotides. Unless otherwise indicated, a particular nucleicacid sequence also implicitly encompasses conservatively modifiedvariants thereof (e.g., degenerate codon substitutions), alleles,orthologs, SNPs, and complementary sequences as well as the sequenceexplicitly indicated. Specifically, degenerate codon substitutions maybe achieved by generating sequences in which the third position of oneor more selected (or all) codons is substituted with mixed-base and/ordeoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991);Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); and Cassol et al.(1992); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The termnucleic acid is used interchangeably with gene, cDNA, and mRNA encodedby a gene.

The terms “polypeptide,” “peptide,” and “protein” are usedinterchangeably herein to include a polymer of amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidue is an artificial chemical mimetic of a corresponding naturallyoccurring amino acid, as well as to naturally occurring amino acidpolymers and non-naturally occurring amino acid polymers. As usedherein, the terms encompass amino acid chains of any length, includingfull-length proteins, truncated forms, or fragments thereof, wherein theamino acid residues are linked by covalent peptide bonds.

The term “amino acid” refers to naturally-occurring and unnatural aminoacids, as well as amino acid analogs and amino acid mimetics thatfunction in a manner similar to the naturally occurring amino acids.

Amino acids may be referred to herein by either their name, theircommonly known three letter symbols or by the one-letter symbolsrecommended by the IUPAC-IUB Biochemical Nomenclature Commission.Additionally, nucleotides may be referred to by their commonly acceptedsingle-letter codes.

The steps of the methods of the present invention do not necessarilyhave to be performed in the particular order in which they arepresented. A person of ordinary skill in the art would understand thatother orderings of the steps of the methods of the invention areencompassed within the scope of the present invention.

Brackets, “[ ]” indicate that the species within the brackets arereferred to by their concentration.

III. Description of the Embodiments

The present invention provides novel indirect homogeneous mobility shiftassays for detecting and measuring the presence or level of a biologicin a sample. The assays of the present invention are particularlyadvantageous for detecting the presence or level of biologics thattarget complex or large antigens including cell surface proteins,transmembrane proteins, heavily glycosylated proteins, and multimericproteins, as well as antigens that cannot be purified, impure antigens,and partially or substantially purified antigens. The present inventionalso provides isolated soluble α4β7 integrin heterodimers and isolatedsoluble IL-12p40 monomers that are suitable for use in the assaysdescribed herein.

In one aspect, the present invention provides a method for determiningthe presence or level of a biologic in a sample, the method comprising:

-   -   (a) contacting the sample with an unlabeled soluble antigen that        binds to the biologic to form an unlabeled complex (e.g., a        plurality of unlabeled complexes) between the antigen and the        biologic in the sample;    -   (b) contacting the sample from step (a) with a labeled form of        the biologic (“labeled biologic”) to form a labeled complex        (e.g., a plurality of labeled complexes) between the antigen and        the labeled biologic;    -   (c) subjecting the (e.g., plurality of) unlabeled and labeled        complexes to size exclusion chromatography to separate the        (e.g., plurality of) unlabeled and labeled complexes from free        labeled biologic and to detect an amount of the free labeled        biologic; and    -   (d) comparing the amount of the free labeled biologic detected        in step (c) to a standard curve of known amounts of the        biologic, thereby determining the presence or level of the        biologic in the sample.

In some embodiments, the biologic includes antibodies, antibodyfragments, proteins, polypeptides, peptides, fusion proteins,multivalent binding proteins, antibody-drug conjugates, vaccines,nucleic acids, sugars, recombinant forms thereof, engineered formsthereof, and combinations thereof. In particular embodiments, thebiologic comprises an antibody (e.g., a monoclonal antibody) or afragment thereof (e.g., an antigen-binding fragment of a monoclonalantibody) or a conjugate thereof (e.g., an antibody-drug conjugate).Non-limiting examples of antibody-based biologics are shown in Table 1.

In particular embodiments, the method of the present invention detectsthe presence of and/or measures the level of unbound (free) biologic ina sample, e.g., the population of biologic in a sample that is not boundto its (endogenous) target antigen or a fragment thereof.

In certain embodiments, the antigen is a soluble version (e.g., asoluble fragment, variant, or monomeric form) of a membrane-boundprotein, a (heavily) glycosylated protein, a multimeric protein, aninsoluble protein, a protein that is difficult to express or purify,and/or a large protein. In certain instances, the antigen is a solubleextracellular domain of a membrane-bound protein (e.g., a solublecytokine receptor extracellular domain). In certain other instances, theantigen is a soluble homodimer or heterodimer comprising theextracellular domains of two membrane-bound proteins (e.g., a solubleintegrin heterodimer). In yet other instances, the antigen is a solubleprotein that does not multimerize and remains in monomeric form onceisolated and/or purified (e.g., a soluble cytokine variant with one ormore cysteine residues mutated to minimize or eliminate the formation ofmultimers).

In some embodiments, the antigen is a soluble fragment (e.g.,extracellular domain) of a cell surface molecule such as, e.g., a celladhesion molecule (CAM). Non-limiting examples of CAMs includeimmunoglobulin superfamily (IgSF) CAMs, integrins, cadherins, andselectins.

IgSF CAMs are any of a variety of polypeptides or proteins located onthe surface of a cell that have one or more immunoglobulin-like folddomains, and which function in intercellular adhesion and/or signaltransduction. In many cases, IgSF CAMs are transmembrane proteins.Non-limiting examples of IgSF CAMs include mucosal addressin celladhesion molecule 1 (MADCAM1), neural cell adhesion molecules (NCAMs;e.g., NCAM-120, NCAM-125, NCAM-140, NCAM-145, NCAM-180, NCAM-185, etc.),intercellular adhesion molecules (ICAMs, e.g., ICAM-1, ICAM-2, ICAM-3,ICAM-4, and ICAM-5), vascular cell adhesion molecule-1 (VCAM-1),platelet-endothelial cell adhesion molecule-1 (PECAM-1), L1 celladhesion molecule (L1CAM), cell adhesion molecule with homology to L1CAM (close homolog of L1) (CHL1), sialic acid binding Ig-like lectins(SIGLECs; e.g., SIGLEC-1, SIGLEC-2, SIGLEC-3, SIGLEC-4, etc.), nectins(e.g., Nectin-1, Nectin-2, Nectin-3, etc.), and nectin-like molecules(e.g., Nec1-1, Nec1-2, Nec1-3, Nec1-4, and Nec1-5.

Integrins are transmembrane αβ heterodimers and at least 18 α and eightβ subunits are known in humans, generating 24 heterodimers. The α and βsubunits have distinct domain structures, with extracellular domainsfrom each subunit contributing to the ligand-binding site of theheterodimer. Non-limiting examples of integrins include α₁β₁, α₂β₁,α₃β₁, α₄β₁, α₅β₁, α₆β₁, α₇β₁, α₈β₁, α₉β₁, α₁₀β₁, α₁₁β₁, α_(v)β₁,α_(v)β₃, α_(v)β₅, α_(v)β₆, α_(v)β₈, α_(IIb)β₃, α₄β₇, β_(E)β₇, α₆β₄,α_(L)β₂, α_(M)β₂, α_(X)β₂, and α_(D)β₂.

In particular embodiments, the antigen is an α4β7 integrin and thebiologic is an anti-α4β7 integrin drug such as vedolizumab (VLM). Incertain instances, the soluble fragment of the α4β7 integrin that bindsto the anti-α4β7 integrin drug comprises an α4 fragment comprising anamino acid sequence having at least 80% identity to SEQ ID NO:1 or SEQID NO:3 and/or a β7 fragment comprising an amino acid sequence having atleast 80% identity to SEQ ID NO: 2 or SEQ ID NO:4.

In other embodiments, the antigen is an α4β1 integrin and the biologicis an anti-α4β1 integrin drug such as natalizumab. In certain instances,the soluble fragment of the α4β1 integrin that binds to the anti-α4β1integrin drug comprises a heterodimer of the extracellular domains ofthe α4 and β1 subunits.

Cadherins are calcium-dependent transmembrane proteins that playimportant roles in cell adhesion, forming adherens junctions to bindcells within tissues together. Non-limiting examples of cadherinsinclude E-cadherin, N-cadherin, N-cadherin 2, and P-cadherin.

Selectins are heterophilic CAMs that bind fucosylated carbohydrates,e.g., mucins. The three family members are E-selectin (endothelial),L-selectin (leukocyte), and P-selectin (platelet).

In other embodiments, the antigen is a soluble fragment (e.g.,extracellular domain) of a cell surface molecule such as, e.g., acytokine receptor.

Non-limiting examples of cytokine receptors include type I cytokinereceptors, type II cytokine receptors, members of the immunoglobulin(Ig) superfamily, tumor necrosis factor receptors, chemokine receptors,and TGFβ receptors. Examples of type I cytokine receptors include, butare not limited to, interleukin receptors (e.g., IL-2 receptor, IL-3receptor, IL-4 receptor, IL-5 receptor, IL-6 receptor, IL-7 receptor,IL-9 receptor, IL-11 receptor, IL-12 receptor, IL-13 receptor, IL-15receptor, IL-21 receptor, IL-23 receptor, IL-27 receptor, etc.), colonystimulating factor receptors (e.g., erythropoietin receptor, GM-CSFreceptor, G-CSF receptor, etc.), hormone receptors or neuropeptidereceptors (e.g., growth hormone receptor, prolactin receptor, etc.), andother cytokine receptors such as oncostatin M receptor and leukemiainhibitory factor receptor. Examples of type II cytokine receptorsinclude, but are not limited to, interferon receptors (e.g.,interferon-alpha/beta receptor, interferon-gamma receptor, etc.) andinterleukin receptors (e.g., IL-10 receptor, IL-20 receptor, IL-22receptor, IL-28 receptor, etc.). Examples of immunoglobulin (Ig)superfamily receptors include, but are not limited to, IL-1 receptor,CSF1, c-kit receptor, and IL-18 receptor. Examples of tumor necrosisfactor receptors include, but are not limited to, TNF receptor (CD120),lymphotoxin β receptor, CD134, CD40, FAS, TNFRSF6B, CD27, CD30, CD137,TNFRSF10A, TNFRSF10B, TNFRSF10C, TNFRSF10D, RANK, osteoprotegerin,TNFRSF12A, TNFRSF13B, TNFRSF13C, TNFRSF14, nerve growth factor receptor,TNFRSF17, TNFRSF18, TNFRSF19, TNFRSF21, TNFRSF25, and ectodysplasin A2receptor. Examples of chemokine receptors include, but are not limitedto, CXC chemokine receptors, CC chemokine receptors, C chemokinereceptors, and CX3C chemokine receptors. Examples of TGFβ receptorsinclude, but are not limited to, TGFβ receptor 1, TGFβ receptor 2, andTGFβ receptor 3.

In certain embodiments, the antigen is an IL-6 receptor and the biologicis an anti-IL-6 receptor drug such as tocilizumab. In certain instances,the soluble fragment of the IL-6 receptor that binds to the anti-IL-6receptor drug comprises an extracellular domain of the IL-6 receptor.

In yet other embodiments, the antigen is a soluble fragment (e.g.,extracellular domain) of a cluster of differentiation (CD) molecule.Non-limiting examples of CD molecules include CD3, CD4, CD8, CD11a,CD11b, CD14, CD15, CD16, CD19, CD20, CD22, CD24, CD25, CD30, CD31, CD34,CD38, CD45, CD56, CD61, CD91, CD114, CD117, CD182, and the like. Incertain instances, the biologic that binds to a soluble fragment of a CDmolecule is a member selected from the group consisting of visilizumab,priliximab, rituximab, ofatumumab, obinutuzumab, ibritumomab tiuxetan,tositumomab, ocrelizumab, veltuzumab, daclizumab, and combinationsthereof.

In some embodiments, the antigen is a cytokine or a monomer thereof(e.g., a soluble cytokine variant with one or more cysteine residuesmutated to minimize or eliminate the formation of multimers).

Non-limiting examples of cytokines include TNFα, TNF-related weakinducer of apoptosis (TWEAK), osteoprotegerin (OPG), IFN-α, IFN-β,IFN-γ, interleukins (e.g., IL-1α, IL-1β, IL-1 receptor antagonist(IL-1ra), IL-2, IL-4, IL-5, IL-6, soluble IL-6 receptor (sIL-6R), IL-7,IL-8, IL-9, IL-10, IL-12, IL-13, IL-15, IL-17, IL-23, and IL-27),adipocytokines (e.g., leptin, adiponectin, resistin, active or totalplasminogen activator inhibitor-1 (PAI-1), visfatin, and retinol bindingprotein 4 (RBP4)), and the like.

In particular embodiments, the cytokine is a p40 subunit of IL-12 orIL-23 and the biologic is an anti-IL-12p40 drug such as ustekinumab(UTK). In certain instances, the cytokine is a p40 variant whichcomprises one or more cysteine residues mutated to minimize or eliminatethe formation of multimers. In some instances, the p40 variant comprisesan amino acid sequence having at least 80% identity to SEQ ID NOS:6, 7,11, 12 or 13.

In other embodiments, the cytokine is TNFα and the biologic is ananti-TNFα drug. Non-limiting examples of anti-TNFα drugs includeREMICADE® (infliximab), HUMIRA® (adalimumab), ENBREL® (etanercept),CIMZIA® (certolizumab pegol), SIMPONI® (golimumab), and combinationsthereof.

The soluble antigens described herein can be produced by any methodknown to one of ordinary skill in the art, such as but not limited to,synthetic methods, such as solid phase and liquid phase synthesis, orrecombinant biology methods.

In some embodiments, the sample is a whole blood, serum, or plasmasample, e.g., obtained from a subject receiving biologic therapy. Inpreferred embodiments, the sample is serum. In particular embodiments,the subject has a disease or disorder such as, e.g., an autoimmunedisease (e.g., rheumatoid arthritis), an inflammatory disease (e.g.,inflammatory bowel disease (IBD) such as Crohn's disease (CD) orulcerative colitis (UC)), or cancer.

In particular embodiments, the standard curve is generated by incubatingthe antigen and the labeled biologic with a (e.g., two-fold) serialdilution of known amounts of the biologic. In certain embodiments, thearea under the curve (AUC) of the free labeled biologic is plottedagainst (e.g., the logarithm of) known amounts of the biologic obtainedfrom the standard curve, and the level of the biologic in the sample iscalculated by interpolation, e.g., based upon the size of the peak areaof the free labeled biologic. In other embodiments, a ratio of the freelabeled biologic to a loading control (e.g., free label) is determinedand used to normalize the level of the biologic in the sample from thestandard curve.

In certain embodiments, the size exclusion chromatography (SEC) is sizeexclusion-high performance liquid chromatography (SE-HPLC). Inparticular embodiments, the (e.g., plurality of) unlabeled and labeledcomplexes are eluted first through a stationary phase, followed by thefree labeled biologic. The underlying principle of SEC is that moleculesor complexes of different sizes will elute (filter) through a stationaryphase at different rates. This results in the separation of a solutionof molecules or complexes based on size. Provided that all the moleculesor complexes are loaded simultaneously or near simultaneously, moleculesor complexes of the same size elute together. Each size exclusion columnhas a range of molecular weights that can be separated. The exclusionlimit defines the molecular weight at the upper end of this range and iswhere molecules or complexes are too large to be trapped in thestationary phase. The permeation limit defines the molecular weight atthe lower end of the range of separation and is where molecules orcomplexes of a small enough size can penetrate into the pores of thestationary phase completely and all molecules or complexes below thismolecular mass are so small that they elute as a single band.

In some instances, the eluent is collected in constant volumes, orfractions. The more similar the molecules or complexes are in size, themore likely they will be in the same fraction and not detectedseparately. Preferably, the collected fractions are examined byspectroscopic techniques to determine the concentration of the moleculesor complexes eluted. Typically, the spectroscopy detection techniquesuseful in the present invention include, but are not limited to,fluorometry, refractive index (RI), and ultraviolet (UV). In certaininstances, the elution volume decreases roughly linearly with thelogarithm of the molecular hydrodynamic volume (i.e., heaver moleculesor complexes come off first).

A biologic (e.g., therapeutic antibody) can be labeled with any of avariety of detectable group(s). In certain embodiments, a biologic islabeled with a fluorophore or a fluorescent dye. In other embodiments, abiologic is labeled with a luminescent tag, a metal, a radionuclide, andthe like. Specific immunological binding of an antigen to a labeledbiologic or the amount of free labeled biologic can be detected directlyor indirectly. A signal from the direct or indirect label can beanalyzed, e.g., using a spectrophotometer to detect color from achromogenic substrate, a radiation counter to detect radiation such as agamma counter for detection of ¹²⁵I, or a fluorometer to detectfluorescence in the presence of light of a certain wavelength.

Non-limiting examples of fluorophores or fluorescent dyes include thoselisted in the Molecular Probes Catalogue, which is herein incorporatedby reference (see, R. Haugland, The Handbook—A Guide to FluorescentProbes and Labeling Technologies, 10^(th) Edition, Molecular probes,Inc. (2005)). Such exemplary fluorophores or fluorescent dyes include,but are not limited to, Alexa Fluor® dyes such as Alexa Fluor® 350,Alexa Fluor® 405, Alexa Fluor® 430, Alexa Fluor® 488, Alexa Fluor® 514,Alexa Fluor® 532, Alexa Fluor® 546, Alexa Fluor® 555, Alexa Fluor® 568,Alexa Fluor® 594, Alexa Fluor® 610, Alexa Fluor® 633, Alexa Fluor® 635,Alexa Fluor® 647, Alexa Fluor® 660, Alexa Fluor® 680, Alexa Fluor® 700,Alexa Fluor® 750, and/or Alexa Fluor® 790, as well as other fluorophoresincluding, but not limited to, Dansyl Chloride (DNS-Cl),5-(iodoacetamida)fluoroscein (5-IAF), fluoroscein 5-isothiocyanate(FITC), tetramethylrhodamine 5- (and 6-)isothiocyanate (TRITC),6-acryloyl-2-dimethylaminonaphthalene (acrylodan),7-nitrobenzo-2-oxa-1,3-diazol-4-yl chloride (NBD-Cl), ethidium bromide,Lucifer Yellow, 5-carboxyrhodamine 6G hydrochloride, Lissamine rhodamineB sulfonyl chloride, Texas Red™ sulfonyl chloride, BODIPY™,naphthalamine sulfonic acids (e.g., 1-anilinonaphthalene-8-sulfonic acid(ANS), 6-(p-toluidinyl)naphthalen-e-2-sulfonic acid (TNS), and thelike), Anthroyl fatty acid, DPH, Parinaric acid, TMA-DPH, Fluorenylfatty acid, fluorescein-phosphatidylethanolamine, TexasRed-phosphatidylethanolamine, Pyrenyl-phophatidylcholine,Fluorenyl-phosphotidylcholine, Merocyanine 540,1-(3-sulfonatopropyl)-4-[β-[2[(di-n-butylamino)-6naphthyl]vinyl]pyridinium betaine (Naphtyl Styryl), 3,3′dipropylthiadicarbocyanine (diS-C₃-(5)), 4-(p-dipentylaminostyryl)-1-methylpyridinium (di-5-ASP), Cy-3 Iodo Acetamide,Cy-5-N-Hydroxysuccinimide, Cy-7-Isothiocyanate, rhodamine 800, IR-125,Thiazole Orange, Azure B, Nile Blue, Al Phthalocyanine, Oxaxine 1,4′,6-diamidino-2-phenylindole (DAPI), Hoechst 33342, TOTO, AcridineOrange, Ethidium Homodimer, N(ethoxycarbonylmethyl)-6-methoxyquinolinium(MQAE), Fura-2, Calcium Green, Carboxy SNARF-6, BAPTA, coumarin,phytofluors, Coronene, metal-ligand complexes, IRDye® 700DX, IRDye® 700,IRDye® 800RS, IRDye® 800CW, IRDye® 800, Cy5, Cy5.5, Cy7, DY 676, DY680,DY682, DY780, and mixtures thereof. Additional suitable fluorophoresinclude enzyme-cofactors; lanthanide, green fluorescent protein, yellowfluorescent protein, red fluorescent protein, or mutants and derivativesthereof.

Typically, the fluorescent group is a fluorophore selected from thecategory of dyes comprising polymethines, pthalocyanines, cyanines,xanthenes, fluorenes, rhodamines, coumarins, fluoresceins and BODIPY™.

In certain embodiments, the fluorescent group is a near-infrared (NIR)fluorophore that emits in the range of between about 650 to about 900nm. Use of near infrared fluorescence technology is advantageous inbiological assays as it substantially eliminates or reduces backgroundfrom auto fluorescence of biosubstrates. Another benefit to the near-IRfluorescent technology is that the scattered light from the excitationsource is greatly reduced since the scattering intensity is proportionalto the inverse fourth power of the wavelength. Low backgroundfluorescence and low scattering result in a high signal to noise ratio,which is essential for highly sensitive detection. Furthermore, theoptically transparent window in the near-IR region (650 nm to 900 nm) inbiological tissue makes NIR fluorescence a valuable technology for invivo imaging and subcellular detection applications that require thetransmission of light through biological components. Within aspects ofthis embodiment, the fluorescent group is preferably selected form thegroup consisting of IRDye® 700DX, IRDye® 700, IRDye® 800RS, IRDye®800CW, IRDye® 800, Alexa Fluor® 660, Alexa Fluor® 680, Alexa Fluor® 700,Alexa Fluor® 750, Alexa Fluor® 790, Cy5, Cy5.5, Cy7, DY 676, DY680,DY682, and DY780. In certain embodiments, the near infrared group isIRDye® 800CW, IRDye® 800, IRDye® 700DX, IRDye® 700, or Dynomic DY676.

Fluorescent labeling can be accomplished using a chemically reactivederivative of a fluorophore. Common reactive groups include aminereactive isothiocyanate derivatives such as FITC and TRITC (derivativesof fluorescein and rhodamine), amine reactive succinimidyl esters suchas NHS-fluorescein, and sulfhydryl reactive maleimide activated fluorssuch as fluorescein-5-maleimide, many of which are commerciallyavailable. Reaction of any of these reactive dyes with a biologicresults in a stable covalent bond formed between a fluorophore and abiologic.

In certain instances, following a fluorescent labeling reaction, it isoften necessary to remove any non-reacted fluorophore from the labeledtarget molecule. This is often accomplished by size exclusionchromatography, taking advantage of the size difference betweenfluorophore and labeled protein.

Reactive fluorescent dyes are available from many sources. They can beobtained with different reactive groups for attachment to variousfunctional groups within the target molecule. They are also available inlabeling kits that contain all the components to carry out a labelingreaction. In certain instances, Alexa Fluor® 488 NHS ester is used fromLife Technologies (Cat. No. A-10235).

IV. Indirect Homogeneous Mobility Shift Assays

The present invention provides novel indirect assays for detecting andmeasuring the presence or level of a biologic (“drug”) in a sample usingsize exclusion chromatography. The assays of the present invention areparticularly advantageous for detecting the presence or level of drugsthat target complex or large antigens including cell surface proteins,transmembrane proteins, heavily glycosylated proteins, and multimericproteins, as well as antigens that cannot be purified, impure antigens,and partially or substantially purified antigens. The antigens are notlabeled and thus patient drug/antigen complexes do not appear in thechromatogram. The principle behind the indirect assays is that theamount of patient drug determines how much unlabeled antigen remainsfree to bind to a labeled version of the drug. By tracking changes inthe area of the free (unbound) labeled drug, one can determine how muchpatient drug is present.

In certain aspects, the first step of the indirect assays describedherein comprises incubating a sample (e.g., serum) containingtherapeutic drug (e.g., vedolizumab (VDZ)) with a fixed amount ofantigen to the drug (e.g., soluble α4β7). In the second step, a fixedamount of labeled drug (e.g., VDZ coupled with Alexa Fluor® 488) isadded. The amount of therapeutic drug in the sample determines how muchantigen remains free and available to bind the labeled drug. This, inturn, determines how much labeled drug is free. Since the peak area ofthe free labeled drug is proportional to the amount of therapeutic drugin the sample, one can quantify the amount of therapeutic drug byinterpolation against a standard curve containing known amounts of drug.

The following description of the principles of the indirect assays ofthe invention uses vedolizumab (VDZ) as the therapeutic drug forillustrative purposes only (see, FIG. 1 ), and is not intended to limitthe scope of the assay methodology for detecting or measuring thepresence or level of other biologics in patient samples:

-   -   1. To each patient sample (e.g., serum), fixed amounts of        antigen (e.g., soluble α4β7) and labeled VDZ are added. The        amount of antigen and labeled VDZ can be added to each sample in        a controlled ratio. For example, adding an amount of antigen        which would bind up about 75-80% of the labeled VDZ provides        optimal sensitivity without limiting the dynamic range of the        assay. The ratio of antigen to labeled VDZ was determined by        titrating the antigen with a fixed amount of labeled VDZ so that        when the antigen is added to the labeled VDZ, the peak of free        labeled VDZ is reduced by about 75-80% (see, FIG. 2 ).    -   2. Quantification can be performed by tracking the increase of        the labeled VDZ peak area (R_(t)=7.5-8.5 min). This area is        proportional to the amount of therapeutic drug present.        Tris-blocked Alexa488 can be added to labeled VDZ stock        solutions as a loading control. Raw chromatograms can be        collected in Agilent ChemStation and then exported to the        program “R” for automated analysis. The standard curve can be        generated by plotting the labeled VDZ peak area as a function of        the log of known VDZ sample concentrations. A 10-point standard        curve can be used and fitted with a 5-parameter logistic (5-PL)        model to account for asymmetry. Unknowns can be determined from        the standard curve by interpolation.

In certain embodiments, the ratio of antigen to labeled drug that isadded to a sample is an amount of each reagent that provides the bestcompromise between the low-end sensitivity needed as well as a dynamicrange that enables the measurement of drug in patient samples withoutrequiring dilutions. As a non-limiting example, the ratio of antigen tolabeled drug that is added to a sample is an amount of antigen thatbinds up about 75% to about 80% (e.g., about 75%, 76%, 77%, 78%, 79%, or80%) of the labeled drug. In some instances, the ratio of antigen tolabeled drug that is added to a sample is an amount of antigen thatbinds up at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or95% of the labeled drug. In other instances, the ratio of antigen tolabeled drug that is added to a sample is an amount of antigen thatbinds up about 50% to about 90%, about 60% to about 90%, about 70% toabout 90%, about 80% to about 90%, about 50% to about 80%, about 60% toabout 80%, about 70% to about 80%, about 50% to about 70%, about 60% toabout 70%, or about 50% to about 60% of the labeled drug. The ratio ofantigen to labeled drug can be determined by titrating the antigen witha fixed amount of labeled drug so that when the antigen is added to thelabeled drug, the peak of free labeled drug is reduced by a desiredpercent (e.g., about 75-80%).

In certain other embodiments, the dynamic range of the indirect assaysdescribed herein can be improved by proportionately increasing theamount of both antigen and labeled drug that is added to a sample. Insome instances, the amount of both antigen and labeled drug can be about1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.5-fold,3-fold, 3.5-fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, 6-fold, 6.5-fold,7-fold, 7.5-fold, 8-fold, 8.5-fold, 9-fold, 9.5-fold, or 10-fold morethan a reference amount of antigen and labeled drug. As a non-limitingexample, the reference amount of labeled VDZ can be about 75 ng and theincreased amount of labeled VDZ can be about 120 ng (i.e., 1.6-fold morethan the reference amount).

In some embodiments, the lower limit of quantitation (LLOQ) of theindirect assays described herein is about 0.125 μg/mL, 0.25 μg/mL, 0.375μg/mL, 0.5 μg/mL, 0.625 μg/mL, 0.75 μg/mL, 0.875 μg/mL, 1 μg/mL, 1.25μg/mL, 1.5 μg/mL, 1.75 μg/mL, 2 μg/mL, 3 μg/mL, 4 μg/mL, or 5 μg/mL. Inother embodiments, the upper limit of quantitation (ULOID) of theindirect assays described herein is about 8 μg/mL, 9 μg/mL, 10 μg/mL, 11μg/mL, 12 μg/mL, 13 μg/mL, 14 μg/mL, 15 μg/mL, 16 μg/mL, 17 μg/mL, 18μg/mL, 19 μg/mL, 20 μg/mL, 21 μg/mL, 22 μg/mL, 23 μg/mL, 24 μg/mL, 25μg/mL, 26 μg/mL, 27 μg/mL, 28 μg/mL, 29 μg/mL, 30 μg/mL, 35 μg/mL, 40μg/mL, 45 μg/mL, or 50 μg/mL. In particular embodiments, the LLOQ isabout 1 μg/mL and the ULOQ is about 25 μg/mL.

V. Soluble α4β7 Integrin Polypeptide Antigens

In one aspect, the present invention provides an isolated soluble α4integrin polypeptide comprising an amino acid sequence having at least80% sequence identity, e.g., at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%sequence identity, to SEQ ID NO: 1. In some embodiments, the isolatedsoluble α4 integrin polypeptide comprises β-propeller repeats (i.e.,repeats 1-7) and a thigh domain of the human α4 integrin extracellulardomain (see, FIG. 13 ; “α4Δ620”), or a fragment thereof. In otherembodiments, the isolated soluble α4 integrin polypeptide comprisesβ-propeller repeats, a thigh domain, and one or both Calf domains (i.e.,Calf-1 and/or Calf-2) of the human α4 integrin extracellular domain, ora fragment thereof. In yet other embodiments, the isolated soluble α4integrin polypeptide is a truncated receptor comprising the entire humanα4 integrin extracellular domain. The isolated soluble α4 integrinpolypeptide described herein includes a ligand binding domain or aportion thereof.

In some embodiments, the isolated soluble α4 integrin polypeptide alsoincludes an ACID peptide. Such a peptide may have an amino acid sequencehaving at least 80% sequence identity, e.g., at least 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99% or 100% sequence identity, to SEQ ID NO:8. An ACID peptidecan form an α-helical coiled-coil conformation with a BASE peptide. Insome embodiments, the ACID peptide includes a cysteine residue that canform a disulfide bridge with a cysteine residue on the BASE peptide.Acid coiled-coil region peptides (ACID peptides) and basic coiled-coilregion peptides (BASE peptides) are described in, e.g., O'Shea et al.,Curr Biol, 1993, 3:658-667, Jun et al., Proc Natl Acad Sci U.S.A., 2001,98(12):6830-6835, Takagi et al., Nat Struct. Biol., 2001, 8:412-416,Nishida et al., Immunity, 2006, 25:583-594, and Dong et al.,Biochemistry, 2012, 51(44):8814-8828.

In some embodiments, the isolated soluble α4 integrin polypeptideincludes a linker, such as one or more amino acid residues, e.g., 1, 2,3, 4, 5, 6, 7, 8, 9, 10 or more amino acid residues. The linker can belocated between the end of extracellular domain and the ACID peptide.

In some embodiments, the isolated soluble α4 integrin polypeptidecomprises an amino acid sequence having at least 80% sequence identity,e.g., at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity,to SEQ ID NO:3.

The soluble α4 integrin polypeptide can also include an affinity tag orepitope tag, such as a histidine tag, avidin tag, V5 tag, FLAG tag, HAtag, Myc tag, cleavable tag, and the like. In some instances, thesoluble α4 integrin polypeptide can include a fluorescent tag, such asGFP, DsRed, CFP, YFP, RFP, and the like, or other detectable tag, suchas horseradish peroxidase, chloramphenicol acetyltransferase,beta-galactosidase, luciferase, and the like.

In another aspect, the present invention provides an isolated soluble β7integrin polypeptide comprising an amino acid sequence having at least80% sequence identity, e.g., at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%sequence identity, to SEQ ID NO:2. In some embodiments, the isolatedsoluble β7 integrin polypeptide comprises a PSI domain, an I-likedomain, hybrid domains, and an I-EGF 1 domain of the human β7 integrinextracellular domain (see, FIG. 13 ; “β7Δ527”), or a fragment thereof.In other embodiments, the isolated soluble β7 integrin polypeptidecomprises one or more of the PSI domain, I-like domain, and one or bothhybrid domains of the human β7 integrin extracellular domain, or afragment thereof. In yet other embodiments, the isolated soluble β7integrin polypeptide comprises a PSI domain, an I-like domain, hybriddomains, I-EGF domains (i.e., domains 1-4), and optionally a β-tail ofthe human β7 integrin extracellular domain, or a fragment thereof. Infurther embodiments, the isolated soluble β7 integrin polypeptide is atruncated receptor comprising the entire human β7 integrin extracellulardomain. The soluble β7 integrin polypeptide described herein includes aligand binding domain or a portion thereof.

In some embodiments, the isolated soluble β7 integrin polypeptide alsoincludes a BASE peptide. Such a peptide may have an amino acid sequencehaving at least 80% sequence identity, e.g., at least 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99% or 100% sequence identity, to SEQ ID NO:9. A BASE peptidecan form an α-helical coiled-coil conformation with an ACID peptide.

In some embodiments, the isolated soluble β7 integrin polypeptideincludes a protease cleavage site. In some instances, the cleavage siteis a tobacco etch virus (TEV) protease cleavage site. The TEV site caninclude the amino acid sequence EXXYXQ/S, wherein X is any amino acidresidue (SEQ ID NO:10). The TEV site may be located upstream the BASEpeptide.

In some embodiments, the isolated soluble β7 integrin polypeptideincludes a linker, such as one or more amino acid residues, e.g., 1, 2,3, 4, 5, 6, 7, 8, 9, 10 or more amino acid residue. The linker can belocated between the end of the EGF-I domain of the β7 integrinextracellular domain and the cleavage site.

In some embodiments, the isolated soluble β7 integrin polypeptidefurther comprises an affinity tag or epitope tag. Useful affinity orepitope tags include, but are not limited to, a histidine tag, avidintag, V5 tag, FLAG tag, HA tag, Myc tag, cleavable tag, and the like. Insome instances, the soluble β7 integrin polypeptide can include afluorescent tag, such as GFP, DsRed, CFP, YFP, RFP, and the like, orother detectable tag, such as horseradish peroxidase, chloramphenicolacetyltransferase, beta-galactosidase, luciferase, and the like.

In some embodiments, the isolated soluble β7 integrin polypeptidecomprises an amino acid sequence having at least 80% sequence identity,e.g., at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity,to SEQ ID NO:4.

The isolated soluble β7 integrin polypeptide can associate with asoluble α4 integrin polypeptide described herein to form a complex, suchas a covalently linked heterodimer. In some instances, the α4β7 integrincomplex can bind to α4β7 ligands, such as but not limited to VCAM-1 andMAdCAM-1, and to antibodies directed against α4β7 integrin, such as, butnot limited to, vedolizumab, natalizumab, and etrolizumab.

In some aspects, the present invention provides an isolated soluble α4β7integrin polypeptide comprising a soluble α4 integrin polypeptide havingan amino acid sequence that has at least 80% identity, e.g., at least80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity, to SEQ ID NO: 1,wherein the α4 integrin polypeptide is linked to a first member of abinding pair, and a soluble β7 integrin polypeptide having an amino acidsequence that has at least 80% identity, e.g., at least 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99% or 100% sequence identity, to SEQ ID NO: 2, wherein the(37 integrin polypeptide is linked to a second member of the bindingpair.

In some embodiments, the binding pair can be any peptides, molecules,motifs, and compounds that can allow the α4 subunit and β7 subunit toform a heterodimer, such as a covalently linked heterodimer. The α4β7heterodimer is capable of binding to α4β7 ligands, such as, but notlimited to VCAM-1 and MAdCAM-1, and to antibodies directed against α4β7integrin, such as, but not limited to, vedolizumab, natalizumab, andetrolizumab. The soluble α4 integrin polypeptide and the soluble β7integrin polypeptide can heterodimerize via a cysteine bridge or aderivative thereof (see, FIG. 13 ). In some embodiments, the bindingpair is selected from the group consisting of coiled-coil peptides,leucine zipper peptides, dock-and-lock peptides, avidin-biotin, andderivatives thereof. In some instances, the coiled-coil peptides areACID-BASE peptides.

The polypeptides described herein can be produced by any method known toone of ordinary skill in the art, such as but not limited to, syntheticmethods, such as solid phase and liquid phase synthesis, or recombinantbiology methods, such as those described herein.

In other aspects, the present invention provides an expression vectorencoding a soluble α4β7 integrin polypeptide comprising a firstpolynucleotide sequence comprising a nucleic acid sequence encoding asoluble α4 integrin polypeptide having an amino acid sequence that hasat least 80% sequence identity, e.g., at least 80%, 81%, 82%, 83%, 84%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or 100% sequence identity, to SEQ ID NO:1 and a nucleic acidsequence encoding a first member of a binding pair, and a secondpolynucleotide sequence comprising a nucleic acid sequence encoding asoluble (37 integrin polypeptide having an amino acid sequence that hasat least 80% sequence identity, e.g., at least 80%, 81%, 82%, 83%, 84%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or 100% sequence identity, to SEQ ID NO:2 and a nucleic acidsequence encoding a second member of the binding pair. In someembodiments, the first member of the binding pair is an ACID peptide. Insome embodiments, the first member of the binding pair is a BASEpeptide. In some instances, the second polynucleotide sequence furthercomprises a nucleic acid sequence encoding an affinity tag, such as ahistidine tag. In some instances, the second polynucleotide sequencefurther comprises a nucleic acid sequence encoding a protease cleavagesite, such as a TEV site.

In some embodiments, the first polynucleotide sequence comprises anucleic acid sequence encoding a polypeptide having an amino acidsequence that has at least 80% sequence identity, e.g., at least 80%,81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99% or 100% sequence identity, to SEQ ID NO:3. Insome embodiments, the second polynucleotide sequence comprises a nucleicacid sequence encoding a polypeptide having an amino acid sequence thathas at least 80% sequence identity, e.g., at least 80%, 81%, 82%, 83%,84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99% or 100% sequence identity, to SEQ ID NO:4.

In some embodiments, the expression vector is capable of directingexpression of the polynucleotide sequences preferentially in aparticular cell type. The expression vector can be a plasmid, phage,phagemid, cosmid, bacteriophage, baculovirus vector, lentiviral vector,retroviral vector, adenoviral vector, yeast plasmid, and the like. Theexpression vector can also comprise a promoter. Useful promoters includeconstitutive promoters and inducible promoters. The first polynucleotidesequence and/or the second polynucleotide sequence of the expressionvector may be operably linked to a promoter. The promoter can beselected depending on the host cell containing the expression vector orused to generate or produce the soluble α4β7 integrin polypeptideencoded by the expression vector described herein. The expression vectormay include regulatory elements, a selectable marker cassette,antibiotic resistance cassette, or any other component that facilitatesthe expression of the polypeptide by a host cell.

In some embodiments, the first and second polynucleotide sequences arefound in a single expression vector. Such polynucleotide sequence can belocated in a bicistronic expression vector such that an IRES sequence islocated between the first and second polynucleotides sequences in thevector. A single promoter can drive the expression of bothpolynucleotides sequences. In some embodiments, the first polynucleotidesequence is operably linked to the promoter and is located immediatelyupstream from a nucleic acid sequence encoding a ribosomal skip, such asa viral 2A peptide, which is immediately upstream of the secondpolynucleotide sequence. In other embodiments, the second polynucleotidesequence is operably linked to the promoter and is located immediatelyupstream from a nucleic acid sequence encoding a ribosomal skip which isimmediately upstream of the first polynucleotide sequence. The solubleα4 integrin polypeptide and soluble β7 integrin polypeptide can begenerated from one expression vector.

Methods for constructing an expression vector are known to those ofordinary skill in the art. Detailed descriptions of protocols andmethods are described in, e.g., Green, M. R., and Sambrook, J., eds.,Molecular Cloning: A Laboratory Manual, 4th ed., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (2012), Ausubel, F. M., etal., Current Protocols in Molecular Biology (Supplement 99), John Wiley& Sons, New York (2012); Berger and Kimmel, Guide to Molecular CloningTechniques, Methods in Enzymology: Volume 152, Academic Press, Inc., SanDiego, CA, (1987); and PCR Protocols: A Guide to Methods andApplications, Academic Press, San Diego, CA, (1990).

In other aspects, the present invention provides a host cell comprisingany one of the expression vectors encoding a soluble α4β7 integrinpolypeptide described herein. The host cell can be a stable cell line,such as, but not limited to, HEK293 cells, CHO cells, COS cells, Jurkatcells, NIH3T3 cells, and derivatives thereof. The host cell can be abacterial cell, yeast cell, fungal cell, algal cell, plant cell, insectcell, animal cell, mammalian cell, non-human cell, or human cell.Suitable host cells are described in Goeddel, Gene ExpressionTechnology: Methods in Enzymology, 185, Academic Press, San Diego, CA,(1990).

The expression vector can be introduced into the host cell by methodsincluding, but not limited to, transformation, transfection,lipofection, nucleofection, microinjection, electroporation, biolistics,virosomes, liposomes, immunoliposomes, polycation orlipid:polynucleotide conjugates, naked DNA, artificial virions, andagent-enhanced uptake of DNA.

In yet another aspect, the present invention provides a method ofgenerating a soluble α4β7 integrin polypeptide encoded by any one of theexpression vectors described herein. The method comprises (a)introducing the expression vector encoding the soluble α4β7 integrinpolypeptide into a host cell, (b) culturing the resulting host cellunder conditions to produce the soluble α4β7 integrin polypeptide, and(c) isolating the soluble α4β7 integrin polypeptide.

The cells containing the expression vector can be cultured underconditions that allow, promote or induce the production of the solubleα4β7 integrin polypeptide.

The soluble α4 integrin polypeptide, soluble β7 integrin polypeptide andsoluble α4β7 integrin polypeptide can be purified from, for example, acell culture supernatant or soluble fraction of a cell extract,according to standard methods known in the art including, but notlimited to, chromatography (e.g., ion exchange, affinity, hydrophobic,chromatofocusing, and size exclusion), electrophoretic procedures (e.g.,preparative isoelectric focusing), differential solubility (e.g.,ammonium sulfate precipitation), SDS-PAGE, or extraction (see, e.g.,Protein Purification, J. C. Janson and Lars Ryden, eds., VCH Publishers,New York, (1989)) to obtain substantially pure polypeptides. Methods forprotein purification, chromatography, electrophoresis, centrifugation,and crystallization are described in, e.g., Coligan et al., CurrentProtocols in Protein Science, Vol. 1, John Wiley and Sons, Inc., NewYork, (2000).

The soluble recombinant α4β7 integrin polypeptide can complex with itscognate ligand, such as a ligand that specifically binds to wild-type,full-length α4β7 integrin. The soluble recombinant α4β7 integrinpolypeptide can be an antigen for an anti-α4β7 integrin antibody.

VI. Soluble IL-12p40 Polypeptide Antigens

In one aspect, the present invention provides an isolated solubleIL-12p40 polypeptide comprising an amino acid sequence having at least80% sequence identity, e.g., at least 80%, 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100%sequence identity, to SEQ ID NOS:6, 11, 12, or 13. In some embodiments,the polypeptide further comprises an affinity tag. In other embodiments,the isolated soluble IL-12p40 polypeptide comprising an amino acidsequence having at least 80% sequence identity, e.g., at least 80%, 81%,82%, 83%, 84%, 85%, 86%, 8′7%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%,96%, 97%, 98%, 99% or 100% sequence identity, to SEQ ID NO:7. In someembodiments, the polypeptide further comprises an affinity tag. Inparticular embodiments, the soluble IL-12p40 polypeptide is a monomer,and cannot dimerize or form multimers.

In another aspect, the present invention provides an expression vectorencoding a soluble IL-12p40 polypeptide comprising a polynucleotidesequence comprising a nucleic acid sequence encoding an IL-12p40polypeptide having an amino acid sequence that has at least 80% sequenceidentity, e.g., at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequenceidentity, to SEQ ID NOS:6, 11, 12, or 13. The polynucleotide sequencecan further comprise a nucleic acid sequence encoding an affinity tag.Such an affinity tag can be a histidine tag, such as hexahistidine.Other non-limiting examples of affinity tags include an avidin tag, V5tag, FLAG tag, HA tag, Myc tag, cleavable tag, and the like. In someembodiments, the polynucleotide comprising a nucleic acid sequenceencoding an IL-12p40 polypeptide having an amino acid sequence that hasat least 80% sequence identity, e.g., at least 80%, 81%, 82%, 83%, 84%,85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%,99% or 100% sequence identity, to SEQ ID NO:7.

In some embodiments, the expression vector is capable of directingexpression of the polynucleotide sequences preferentially in aparticular cell type. The expression vector can be a plasmid, phage,phagemid, cosmid, bacteriophage, baculovirus vector, lentiviral vector,retroviral vector, adenoviral vector, yeast plasmid, and the like. Theexpression vector can also comprise a promoter. Useful promoters includeconstitutive promoters and inducible promoters. The polynucleotidesequence of the expression vector may be operably linked to a promoter.The promoter can be selected depending on the host cell selected togenerate or produce the soluble IL-12p40 polypeptide encoded by theexpression vector described herein. The expression vector may includeregulatory elements, a selectable marker cassette, antibiotic resistancecassette, or any other component that facilitates the expression of thepolypeptide.

Methods for constructing an expression vector are known to those ofordinary skill in the art. Detailed descriptions of protocols andmethods are described in, e.g., Green, M. R., and Sambrook, J., eds.,Molecular Cloning: A Laboratory Manual, 4th ed., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (2012); Ausubel, F. M., etal., Current Protocols in Molecular Biology (Supplement 99), John Wiley& Sons, New York (2012); Berger and Kimmel, Guide to Molecular CloningTechniques, Methods in Enzymology, Volume 152, Academic Press, Inc., SanDiego, CA (1987); and PCR Protocols: A Guide to Methods andApplications, Academic Press, San Diego, CA, (1990).

In other aspects, the present invention provides a host cell comprisingany one of the expression vectors encoding a soluble IL-12p40polypeptide described herein. The host cell can be a stable cell line,such as, but not limited to, HEK293 cells, CHO cells, COS cells, Jurkatcells, NIH3T3 cells, and derivatives thereof. The host cell can be abacterial cell, yeast cell, fungal cell, algal cell, plant cell, insectcell, animal cell, mammalian cell, non-human cell, or human cell.Suitable host cells are described in Goeddel, Gene ExpressionTechnology: Methods in Enzymology 185, Academic Press, San Diego, CA,1990.

The expression vector can be introduced into the host cell by methodsincluding, but not limited to, transformation, transfection,lipofection, nucleofection, microinjection, electroporation, biolistics,virosomes, liposomes, immunoliposomes, polycation orlipid:polynucleotide conjugates, naked DNA, artificial virions, andagent-enhanced uptake of DNA.

In yet another aspect, the present invention provides method ofgenerating a soluble IL-12p40 polypeptide encoded by any one of theexpression vectors described herein. The method comprises (a)introducing the expression vector encoding the soluble IL-12p40polypeptide into a host cell, (b) culturing the resulting host cellunder conditions to produce the soluble IL-12p40 polypeptide, and (c)isolating the soluble IL-12p40 polypeptide.

The cells containing the expression vector can be cultured underconditions that allow, promote or induce the production of the solubleIL-12p40 polypeptide.

The soluble IL-12p40 polypeptide can be purified from, for example, acell culture supernatant or soluble fraction of a cell extract,according to standard methods known in the art including, but notlimited to, chromatography (e.g., ion exchange, affinity, hydrophobic,chromatofocusing, and size exclusion), electrophoretic procedures (e.g.,preparative isoelectric focusing), differential solubility (e.g.,ammonium sulfate precipitation), SDS-PAGE, or extraction (see, e.g.,Protein Purification, J. C. Janson and Lars Ryden, eds., VCH Publishers,New York, (1989)) to obtain substantially pure polypeptides. Methods forprotein purification, chromatography, electrophoresis, centrifugation,and crystallization are described in, e.g., Coligan et al., CurrentProtocols in Protein Science, Vol. 1, John Wiley and Sons, Inc., NewYork, (2000).

Unlike wild-type IL-12p40, the soluble recombinant IL-12p40 polypeptidedescribed herein cannot form a dimer, trimer, or oligomer. In particularembodiments, the presence of either two cysteine to alaninesubstitutions (SEQ ID NO:6) or two cysteine to serine substitutions (SEQID NO:11) in the wild-type IL-12p40 polypeptide sequence prevents theIL-12p40 antigen from oligomerizing. In other embodiments, the solubleIL-12p40 polypeptide monomer has the wild-type IL-12p40 polypeptidesequence with one cysteine to alanine substitution and one cysteine toalanine substitution (SEQ ID NOS:12 or 13). An anti-IL-12p40 antibody,such as ustekinumab, can specifically bind to the soluble recombinantIL-12p40 polypeptide.

VII. Biologic Therapy

The indirect homogeneous mobility shift assays of the present inventionare suitable for detecting and/or measuring the presence or level of abiologic in a sample from a subject (e.g., a subject receiving biologictherapy). Non-limiting examples of biologics include antibodies,antibody fragments, proteins, polypeptides, peptides, fusion proteins(e.g., Ig fusion proteins or Fc fusion proteins), multivalent bindingproteins (e.g., DVD Ig), antibody-drug conjugates, vaccines, nucleicacids, sugars, recombinant forms thereof, engineered forms thereof, andcombinations thereof.

Examples of antibody-based biologics include, but are not limited to,diagnostic or therapeutic monoclonal antibodies and antigen-bindingfragments or conjugates thereof. In certain embodiments, the antibodycomprises an anti-integrin drug such as an anti-α4β7 integrin drug(e.g., vedolizumab (ENTYVIO™), etrolizumab) and/or an anti-α4β1 integrindrug (e.g., natalizumab (TYSABRI®)). In other embodiments, the antibodycomprises an anti-cytokine drug such as an anti-IL12p40 drug (e.g.,ustekinumab))(STELARA®)). In yet other embodiments, the antibodycomprises an anti-cytokine receptor drug such as an anti-IL-6 receptordrug (e.g., tocilizumab (ACTEMRA®)). In further embodiments, theantibody comprises an anti-CD receptor drug such as an anti-CD3 receptordrug (e.g., visilizumab), an anti-CD4 receptor drug (e.g., priliximab),an anti-CD20 receptor drug (e.g., rituximab (RITUXAN®), ofatumumab(ARZERRA®), obinutuzumab (GAZYVA®), ibritumomab tiuxetan (ZEVALIN®),tositumomab (BEXXAR®), ocrelizumab, veltuzumab, an anti-CD25 receptordrug (e.g., daclizumab (ZENAPAX®)), or combinations thereof. In otherembodiments, the antibody comprises an anti-TNFα drug such as infliximab(REMICADE®), adalimumab (HUMIRA®), etanercept (ENBREL®), golimumab(SIMPONI®), certolizumab pegol (CIMZIA®), or combinations thereof.Additional examples of antibody-based biologics include antibody-drugconjugates such as brentuximab vedotin (ADCETRIS®).

Table 1 provides an exemplary and non-exhaustive list of diagnostic andtherapeutic monoclonal antibodies which have either been approved or arecurrently in development. An extensive list of biologic medicinesincluding monoclonal antibody-based therapeutics and diagnostics inclinical development and approved products is provided in the 2006 PhRMAReport entitled “418 Biotechnology Medicines in Testing Promise toBolster the Arsenal Against Disease” and the 2013 PhRMA Report entitled“Medicines in Development—Biologics,” the disclosures of which arehereby incorporated by reference in their entirety for all purposes.

TABLE 1 Monoclonal Antibodies (mAb) Product Name Company IndicationDigestive Disorders ABT 874 Abbott Laboratories Crohn's disease AMG139/MEDI-2070 Amgen Crohn's disease AMG 181/MEDI-7183 Amgen Crohn'sdisease, ulcerative colitis anrukinzumab (IMA-638) Pfizer ulcerativecolitis anti-IP10 Bristol-Myers Squibb Crohn's disease, ulcerativecolitis clazakizumab (anti-IL6) Bristol-Myers Squibb, Alder Crohn'sdisease Biopharmaceuticals etrolizumab (rhuMAb-07) Genentech ulcerativecolitis GSK1070806 (IL-18 mAb) GlaxoSmithKline inflammatory boweldisease Humira ® (adalimumab) AbbVie Crohn's disease MDX-1100 MillenniumPharmaceuticals ulcerative colitis Nuvion ® (visilizumab) PDL BioPharmaI.V. steroid-refractory ulcerative colitis and Crohn's diseasePF-00547659 Pfizer Crohn's disease PF-04236921 Pfizer Crohn's diseaseQAX576 Novartis Pharmaceuticals Crohn's disease Remicade ® (infliximab)Janssen Biotech Crohn's disease SAR252067 (anti-LIGHT mAb) Sanofi USCrohn's disease, ulcerative colitis SAR339658 (VLA2 antagonist) SanofiUS inflammatory bowel disease Simponi ® (golimumab) Janssen Biotechulcerative colitis Stelara ® (ustekinumab) Janssen Biotech Crohn'sdisease tralokinumab AstraZeneca, MedImmune ulcerative colitis Tysabri ®(natalizumab) Biogen Idec Crohn's disease vedolizumab (MLN0002) TakedaPharmaceuticals Crohn's disease, ulcerative colitis Autoimmune disordersABT-122 AbbVie rheumatoid arthritis Actemra ® (tocilizumab) Genentech,Roche early rheumatoid arthritis, systemic sclerosis AGS-009 ArgosTherapeutics systemic lupus erythematosus (SLE) alemtuzumab Genzymerelapsing-remitting multiple sclerosis AME 527 Applied Molecularrheumatoid arthritis AMG 108 Amgen rheumatoid arthritis AMG557/MEDI-5872 Amgen, AstraZeneca, MedImmune SLE AMG 714 Amgen rheumatoidarthritis AMG 729 Amgen autoimmune diseases AMG 811 Amgen discoid lupuserythematosus, SLE ART 874 Abbott Laboratories multiple sclerosisanti-CD16 mAb MacroGenics immune thrombocytopenic anti-IL17 mAb (RG7624)Genentech autoimmune disorders anti-LINGO (BIIB033) Biogen Idec Multiplesclerosis Benlysta ® (belimumab) GlaxoSmithKline rheumatoid arthritis,SLE, systemic scleroderma BI-695500 (rituximab biosimilar)Boehringer-Ingelheim rheumatoid arthritis Pharmaceuticals BI-695501(adalimumab biosimilar) Boehringer-Ingelheim rheumatoid arthritisPharmaceuticals BT-061 AbbVie, Biotest rheumatoid arthritis Cimzia ®(certolizumab pegol) UCB ankylosing spondylitis, juvenile rheumatoidarthritis clazakizumab (anti-IL6) Bristol-Myers Squibb, Alder rheumatoidarthritis Biopharmaceuticals CNTO-136 (sirukumab) Janssen Biotechrheumatoid arthritis CNTO-1959 Janssen Biotech rheumatoid arthritisdaclizumab (anti-CD25 mAb) AbbVie, Biogen Idec multiple sclerosisepratuzumab Immunomedics, UCB SLE ETI-201 Elusys Therapeutics SLEGSK1223249 (NOGO-A mAb) GlaxoSmithKline multiple sclerosis Humira ®(adalimumab) AbbVie rheumatoid arthritis, ankylosing spondylitis,juvenile rheumatoid arthritis, psoriasis HuZAF ® (fontolizumab) PDLBioPharma, Biogen Idec rheumatoid arthritis Ilaris ® (canakinumab)Novartis Pharmaceuticals systemic juvenile idiopathic arthritis IMMU-106(hCD20) Immunomedics autoimmune diseases mavrilimumab AstraZeneca,MedImmune rheumatoid arthritis MEDI-545 (MDX-1103) Medarex, MedImmunelupus MEDI-546 (anti-IFN-alphaR mAb) AstraZeneca, MedImmune SLE MEDI-551(anti-CD19 mAb) AstraZeneca, MedImmune scleroderma MEDI-570 (anti-ICOSmAb) AstraZeneca, MedImmune SLE MLN 1202 Millennium Pharmaceuticalsmultiple sclerosis NN8209 (anti-C5aR-151 mAb) Novo Nordisk rheumatoidarthritis NN8210 (anti-C5aR-215 mAb) Novo Nordisk rheumatoid arthritisNN8226 (anti-IL-20 mAb) Novo Nordisk rheumatoid arthritis NN8765(anti-NKG2 mAb) Novo Nordisk rheumatoid arthritis NN8828 (anti-IL-21mAb) Novo Nordisk rheumatoid arthritis ocrelizumab (anti-CD20 mAb)Biogen Idec, Genentech, Roche multiple sclerosis, rheumatoid arthritisofatumumab GlaxoSmithKline multiple sclerosis, rheumatoid arthritisOKT3-gamma-1 Johnson & Johnson psoriatic arthritis olokizumab UCBrheumatoid arthritis otelixizumab (anti-CD3 mAb) GlaxoSmithKlinerheumatoid arthritis ozoralizumab (ATN-103) Ablynx rheumatoid arthritispateclizumab (anti-LT alpha mAb) Genentech rheumatoid arthritisPD-360324 Pfizer cutaneous lupus erythematosus PF-04236921 Pfizer SLE,rheumatoid arthritis PF-05280586 (rituximab biosimilar) Pfizerrheumatoid arthritis Prolia ® (denosumab) Amgen rheumatoid arthritisRemicade ® (infliximab) Janssen Biotech rheumatoid arthritis Rituxan ®(rituximab) Genentech, Biogen Idec rheumatoid arthritis, lupus, primaryprogressive multiple sclerosis, SLE, relapsing-remitting multiplesclerosis rontalizumab (RG7415) Genentech SLE SAN-300 (anti-VLA-1antibody) Santams rheumatoid arthritis SAR113244 (anti-CXCR5 mAb) SanofiUS SLE sarilumab (SAR153191) Regeneron Pharmaceuticals, Sanofirheumatoid arthritis US secukinumab (AIN457) Novartis Pharmaceuticalsankylosing spondylitis, rheumatoid arthritis, multiple sclerosissifalimumab (anti-IFN-alpha mAb) AstraZeneca, MedImmune SLE Simponi ®(golimumab) Janssen Biotech rheumatoid arthritis, juvenile rheumatoidarthritis, sarcoidosis, ankylosing spondylitis, psoriatic arthritissiplizumab (MEDI-507) MedImmune psoriasis Soliris ® (eculizumab) AlexionPharmaceuticals severe or refractory myasthenia gravis Stelara ®(ustekinumab) Janssen Biotech rheumatoid arthritis, sarcoidosis, plaquepsoriasis, multiple sclerosis tabalumab (BAFF inhibitor) Eli Lilly SLETRX 1 (anti-CD4) TolerRx cutaneous lupus erythematosus TRX 4 TolerRxpsoriasis Tysarbi ® (natalizumab) Biogen Idec Multiple sclerosisveltuzumab (IMMU-106) Immunomedics, Takeda immune thrombocytopenicPharmaceuticals USA purpura, rheumatoid arthritis VX15 TevaPharmaceuticals, Vaccinex multiple sclerosis XmAb ® 5871 (anti-CD19 mAb)Xencor autoimmune disorders Musculoskeletal Disorders/Arthritis ABT-981AbbVie osteoarthritis AMG 167 Amgen metabolic bone diseases AMG 745Amgen muscular atrophy AMG 827 (brodalumab) AstraZeneca, Amgen psoriaticarthritis blosozumab (LY2541546) Eli Lilly osteoporosis BYM338 NovartisPharmaceuticals sporadic inclusion body myositis, muscular atrophyCimzia ® (certolizumab pegol) UCB psoriatic arthritis clazakizumab(anti-IL6) Bristol-Myers Squibb, Alder psoriatic arthritisBiopharmaceuticals gevokizumab (IL-1B inhibitor mAb) XOMA osteoarthritisof the hand Humira ® (adalimumab) AbbVie spondylarthritis Ilaris ®(canakinumab) Novartis Pharmaceuticals gouty arthritis ixekizumab (IL-17antibody) Eli Lilly psoriatic arthritis LY2495655 (anti-myostatin mAb)Eli Lilly disuse muscular atrophy MCS110 Novartis Pharmaceuticalssynovitis Prolia ® (denosumab) Amgen male osteoporosis, postmenopausalosteoporosis romosozumab (AMG 785) Amgen postmenopausal osteoporosisSAR391786 (REGN1033) Regeneron Pharmaceuticals, Sanofi treatment ofmuscle atrophy post- US orthopedic surgery secukinumab (AIN 457)Novartis Pharmaceuticals psoriatic arthritis, polymyalgia rheumaticaStelara ® (ustekinumab) Janssen Biotech psoriatic arthritis tanezumabPfizer osteoarthritis Cancer and Related Conditions 1311-huA33 LifeScience Pharmaceuticals colorectal cancer 1D09C3 GPC Biotechrelapsed/refractory B-cell lymphomas 8H9 mAb United Therapeuticsmetastatic brain cancer 212-Pb-TCMC-trastuzumab AREVA Med HER2-positivecancer metastasized to the abdominal region AbGn-7 AbGenomicsInternational solid tumors ABT-806 AbbVie solid tumors Actimab-A (M195mAb) Actinium Pharmaceuticals acute myeloid leukemia (AML) Adcetris ®(brentuximab vedotin) Seattle Genetics cutaneous T-cell lymphoma, front-line Hodgkin lymphoma, post- transplant Hodgkin lymphoma relapseprevention, non-Hodgkin lymphoma, non-lymphoma malignancies,CD30-positive hematologic malignancies AGS PSCA mAb Agensys, Merckprostate cancer ALT-836 Altor BioScience, Genentech cancer AME-133vMENTRIK Biotech non-Hodgkin lymphoma AMG 102 Amgen cancer AMG 479 Amgencancer AMG 623 Amgen B-cell chronic lymphocytic leukemia (CLL) AMG 655Amgen cancer AMG 706 Amgen imatinib resistant GIST, advanced thyroidcancer AMG 780 Amgen solid tumors AMG 820 Amgen solid tumors AMG 888(U3-1287) Amgen non-small-cell lung cancer (NSCLC) antibody-drugconjugate (RG7600) Genentech ovarian cancer, pancreatic cancer anti-CD22ADC (RG7593) Genentech, Seattle Genetics diffuse large B-cell lymphoma,non-Hodgkin lymphoma, chronic lymphocytic leukemia (CLL) anti-CD23 MAbBiogen Idec CLL anti-CD45 mAb Actinium Pharmaceuticals AML anti-CD79bADC (RG7596) Genentech, Seattle Genetics diffuse large B-cell lymphoma,non-Hodgkin lymphoma, CLL anti-CD 80 MAb Biogen Idec non-Hodgkin B-celllymphoma anti-CXCR4 Bristol-Myers Squibb hematological malignanciesanti-EGFL7 mAb (RG7414) Genentech metastatic colorectal cancer, NSCLC,solid tumors anti-FGFR3 mAb (RG7444) Genentech solid tumorsanti-HER3/EGFR DAF mAb Genentech colorectal cancer, head and neck(RG7597) cancer anti-idiotype cancer vaccine Viventia Biotech malignantmelanoma anti-lymphotoxin beta receptor Biogen Idec solid tumors mAbanti-PD-L1 Bristol-Myers Squibb cancer anti-PD-L1 mAb (RG7446) Genentechmelanoma, solid tumors anti-PEM MAb Somanta Pharmaceuticals canceranti-STEAP1 ADC (RG7450) Genentech, Seattle Genetics prostate canceranti-Tac(Fv)-E38 immunotoxin National Cancer Institute leukemia,lymphoma APN301 (hu14.18-IL2) Apeiron Biologics malignant melanoma,neuroblastoma in children Archexin ® (RX-0201) Rexahn Pharmaceuticalspancreatic cancer Arzerra ® (ofatumumab) GlaxoSmithKline CLL, diffuselarge B-cell lymphoma, follicular lymphoma ASG-5ME Agensys, SeattleGenetics pancreatic cancer, castration- resistant prostate cancerASG-22ME Agensys, Seattle Genetics solid tumors AV-203 AVEO Oncologysolid tumors Avastin ® (bevacizumab) Genentech, Roche ovarian cancer,HER-2 negative- breast cancer, HER-2 positive breast cancer, high-riskcarcinoid tumors, glioblastoma multiforme, metastatic ovarian cancer,NSCLC, metastatic colorectal cancer AVE 9633 maytansin-loaded anti-Sanofi Aventis AML CD33 mAb bavituximab Peregrine Pharmaceuticals NSCLC,pancreatic cancer, breast cancer, liver cancer, prostate cancer, rectaladenocarcinoma BAX-69 Baxter International solid tumors BAY 79-4620Bayer HealthCare Pharmaceuticals solid tumors BAY 94-9343 BayerHealthCare Pharmaceuticals solid tumors BAY 20-10112 Amgen, BayerHealthCare solid tumors Pharmaceuticals Bexxar ® (tositumomab)GlaxoSmithKline non-Hodgkin lymphoma BHQ880 Novartis Pharmaceuticalsmultiple myeloma BI-505 BioInvent International multiple myelomaBI-836845 Boehringer Ingelheim solid tumors Pharmaceuticals bivatuzumabBoehringer Ingelheim cancer Pharmaceuticals blinatumomab Amgen leukemiaand lymphoma BrevaRex ™ ViRexx breast cancer, multiple myeloma BT-062(indatuximab ravtansine) Biotest multiple myeloma BYM338 NovartisPharmaceuticals cancer-related cachexia Campath ® (alemtuzumab) BerlexLaboratories, Genzyme B-cell chronic lymphocytic leukemia, lymphomacatumaxomab Fresenius Biotech malignant ascites, ovarian cancer CAT 3888Cambridge Antibody Technology hairy cell leukemia CDX-011 (glembatumumabCelldex Therapeutics breast cancer, malignant melanoma vedotin) CDX-1127Celldex Therapeutics hematological malignancies, solid tumorsCEP-37250/KNK-2804 Teva North America, Kyowa adenocarcinoma Hakko KirinPharma ch14.18 mAb United Therapeutics neuroblastoma chimeric mAbNational Cancer Institute neuroblastoma Cixutumumab (LY3012217) EliLilly, Imclone Systems NSCLC CNTO-328 (siltuximab) Janssen Biotech giantlymph node hyperplasia, multiple myeloma, myelodysplastic syndromes,prostate cancer, renal cancer, Cotara ™ mAb TNT PeregrinePharmaceuticals recurrent glioblastoma CP-751871 (figitumumab) Pfizeradrenocortical carcinoma, non- small cell lung cancer CS-1008(tigatuzumab) Daiichi Sankyo pancreatic cancer, colorectal cancer,non-small cell lung cancer, ovarian cancer CSF-1R mAb (IMC-CS4) EliLilly solid tumors CT-011 (pidilizumab) CureTech AML, colorectal cancer,diffuse large B-cell lymphoma, follicular lymphoma, malignant melanomadalotuzumab (MK-0646) Merck breast cancer, neuroendocrine tumors, NSCLCdaratumumab Janssen Biotech multiple myeloma DEDN6526A Genentechmalignant melanoma demcizumab (OMP-21M18) GlaxoSmithKline, OncoMed solidtumors Pharmaceuticals DFRF4539A Genentech multiple myeloma DI17E6(anti-integrin mAb) EMD Serono colorectal cancer, prostate cancer DKN-01Dekkun solid tumors ecromeximab (KW-2871) Life Science Pharmaceuticalsmetastatic melanoma elotuzumab Bristol-Myers Squibb, AbbVie multiplemyeloma EMD 273063 EMD Lexigen solid tumors, malignant melanoma,neuroblastoma, SCLC enavatuzumab AbbVie solid tumors ensituximab(NPC-1C) Neogenix Oncology colorectal cancer, pancreatic cancerepratuzumab Y-90/veltuzumab Immunomedics non-Hodgkin lymphomacombination Erbitux ® (cetuximab) Bristol-Myers Squibb, Eli Lilly,esophageal cancer, colorectal ImClone Systems cancer, squamous cellcancer of the head and neck farletuzumab (MORAb-003) Eisaiplatinum-sensitive ovarian cancer, NSCLC FG-3019 FibroGen pancreaticcancer ficlatuzumab AVEO Oncology glioblastoma, lymphoma, multiplemyeloma, solid tumors flanvotumab (TYRP1 protein) Eli Lilly malignantmelanoma Fzd7 (vantictumab) Bayer HealthCare Pharmaceuticals, solidtumors OncoMed Pharmaceuticals ganitumab Amgen pancreatic cancer, breastcancer, colorectal cancer, sarcoma GC-33/RG7686 Chugai Pharma USA, Rocheliver cancer GMK Progenies Pharmaceuticals prevention of recurrencefollowing surgery to remove primacy melanoma in high-risk patientsGS-6624 (simtuzumab) Gilead Sciences colorectal cancer, pancreaticcancer HCD122 (anti-CD40 mAb) Novartis Pharmaceuticals, XOMA lymphomaHerceptin ® (trastuzumab) Genentech HER2-overexpressing early stage ormetastatic breast cancer HGS-ETR1 (mapatumumab) GlaxoSmithKline livercancer, multiple myeloma, NSCLC, hematologic and solid tumors HGS-TR2JHuman Genome Sciences advanced solid tumors HuC242-DM4 ImmunoGencolorectal, gastrointestinal, NSCLC, pancreatic cancers HuL2G7 GalaxyBiotech solid tumors HuMax-CD4 (zanolimumab) Genmab, Serono cutaneousT-cell lymphoma, non- cutaneous T-cell lymphoma HuMax CD20 (ofatumumab)Genmab CLL, non-Hodgkin lymphoma HuMax-EGFr Genmab head and neck cancerHuM195/rGel Targa Therapeutics AML, CML, myelodysplastic syndromeshuN901-DM1 (lorvotuzumab ImmunoGen SCLC, multiple myeloma, solidmertansine) tumors icrucumab (LY3012212) Eli Lilly, ImClone Systemsbladder cancer, breast cancer, colorectal cancer IMC-TR1 (LY3022859) EliLilly, ImClone Systems solid tumors IMGN529 ImmunoGen non-Hodgkinlymphoma IMGN853 ImmunoGen solid tumors IMMU-102 (epratuzumab Y-90)Immunomedics non-Hodgkin lymphoma inotuzumab ozogamicin (CMC-544)Pfizer, UCB aggressive non-Hodgkin lymphoma, ALL Iomab-B (anti-CD45 mAb)Actinium Pharmaceuticals AML J 591 Lu-177 BZL Biologics prostate cancerKB004 KaloBios Pharmaceuticals hematological malignancies LFA102Novartis Pharmaceuticals, XOMA breast cancer, prostate cancer lirilumab(anti-KIR) Bristol-Myers Squibb cancer LY2495655 (anti-myostatin mAb)Eli Lilly cancer cachexia LY2875358 (c-met mAb) Eli Lilly cancerM195-bismuth 213 conjugate Actinium Pharmaceuticals AML M200(volociximab) PDL BioPharma, Biogen Idec advanced solid tumors MAbHeFi-1 National Cancer Institute lymphoma, non-Hodgkin lymphoma MABp1XBiotech cancer-related cachexia, advanced cancer, leukemia MDX-060(iratumumab) Medarex Hodgkin's disease, anaplastic large- cell-lymphomaMDX-070 Medarex prostate cancer MDX-214 Medarex EGFR-expressing cancersMEDI-522 MedImmune T-cell lymphoma, melanoma, prostate cancer, solidtumors MEDI-551 (anti-CD19 mAb) AstraZeneca, MedImmune hematologicalmalignancies MEDI-573 (anti-IGF mAb) AstraZeneca, MedImmune solid tumorsMEDI-575 (anti-PDGFRα mAb) AstraZeneca, MedImmune glioblastoma, NSCLCMEDI-0639 (anti-DLL-4 mAb) AstraZeneca, MedImmune solid tumors MEDI-3617(anti-ANG-2 mAb) AstraZeneca, MedImmune solid tumors MEDI-4736(anti-CD274 mAb) AstraZeneca, MedImmune cancer MEDI-6469 (anti-OX40 mAb)AgonOx, AstraZeneca, solid tumors MedImmune MGA271 (anti-B7-H3)MacroGenics solid tumors MGAH22 (anti-HER2) MacroGenics solid tumorsmilatuzumab Immunomedics CLL milatuzumab-DOX Immunomedics multiplemyeloma MINT1526A Genentech solid tumors MK-3475 Merck malignantmelanoma, NSCLC MLN0264 (GCC antibody drug Millennium Pharmaceuticalsgastrointestinal cancer conjugate) mogamulizimab Kyowa Hakko KirinPharma cutaneous T-cell lymphoma, adult T-cell lymphoma, T-cell leukemiaMORAb 003 Eisai ovarian cancer MORAb-004 Eisai colorectal cancer,melanoma, sarcoma MORAb-009 (amatuximab) Eisai mesothelioma moxetumomabpasudotox AstraZeneca, MedImmune hematological malignancies Mylotarg ™(gemtuzumab Wyeth acute myeloid leukemia ozogamicin) necitumumabBristol-Myers Squibb, Eli Lilly, NSCLC ImClone Systems neuradiab BradmerPharmaceuticals glioblastoma nimotuzumab InnoMab PIE glioma, squamouscell carcinomas of the head and neck, recurrent or refractory high grademalignant glioma, anaplastic astrocytomas, glioblastomas and diffuseintrinsic pontine glioma nivolumab (anti-PD1) Bristol-Myers Squibbmelanoma, NSCLC, renal cell carcinoma, solid tumors obinutuzumab (GA101)Biogen Idec, Genentech CLL, diffuse large B-cell lymphoma, non-Hodgkinlymphoma olamtumab (LY3012207) Eli Lilly, ImClone Systems glioblastomaOMP-52M51 (anti-Notch 1) GlaxoSmithKline, OncoMed hematologicalmalignancies Pharmaceuticals OMP-59R5 (anti-Notch 2/3) GlaxoSmithKline,OncoMed pancreatic cancer Pharmaceuticals onartuzumab (anti-c-met- mAb)Genentech metastatic NSCLC oregovomab Quest Pharmatech ovarian cancerPAM 4 Merck pancreatic cancer panitumumab (rIIuMAb EGFr) Abgenixcolorectal cancer Perjeta ™ (pertuzumab) Genentech early HER2-positivebreast cancer, HER2-positive metastatic breast cancer, HER2-positivegastric cancer, ovarian cancer PF-03446962 Pfizer solid tumorsPF-04605412 Pfizer solid tumors PF-05082566 Pfizer cancer, lymphomaPF-05280014 (trastuzumab biosimilar) Pfizer metastatic breast cancerPSMA-ADC Progenics Pharmaceuticals prostate cancer R1550 RadioTheraCIMRoche, YM BioSciences metastatic breast cancer, glioma mmucirumab(LY3009806) Eli Lilly, ImClone Systems breast cancer, colorectal cancer,gastric cancer RAV 12 Raven Biotechnologies cancer Redectane ®(girentuximab I-124) Wilex AG diagnosis of kidney cancer REGN1400Regeneron Pharmaceuticals cancer Rencarex ® G250 Wilex AG renal cancerRG7116 Roche solid tumors RG7155 Roche solid tumors RG7160 (humAb EGFR)Roche colorectal cancer RG7212 Roche solid tumors RG7356 (anti-CD44 mAb)Roche AML, solid tumors RG7458 (antibody-drug conjugate) Genentech,Seattle Genetics ovarian cancer RIGScan ™ Navidea Biopharmaceuticalsdiagnosis of colorectal cancer rilotumumab Amgen colorectal cancer,gastric cancer, prostate cancer, SCLC Rituxan ® (rituximab) Genentechdiffuse large B-cell lymphoma, B- cell non-Hodgkin lymphoma, indolentnon-Hodgkin lymphoma induction therapy, relapsed or refractory CLL RON8mAb Eli Lilly, ImClone Systems cancer SAR3419 (maytansin-loaded anti-Sanofi US ALL, non-Hodgkin lymphoma CD19 mAb) SAR153192 (REGN 421)Regeneron Pharmaceuticals, Sanofi cancer (anti-DLL4 mAb) US SAR256212(MM-121) Merrimack Pharmaceuticals, Sanofi breast cancer, solid tumors(anti-ErbB3 mAb) US SAR307746 (REGN910) Regeneron Pharmaceuticals,Sanofi solid tumors (anti-angiopoietin-2 mAb) US SAR566658 Sanofi USDS6-positive solid tumors (maytansin-loaded anti-D56) SAR650984 SanofiUS hematological malignancies (anti-CD38 naked mAb) SGN30 SeattleGenetics cutaneous anaplastic large-cell lymphoma, systemic anaplasticlarge-cell lymphoma, Hodgkin's disease SGN-33 (lintuzumab) SeattleGenetics AML, myelodysplastic syndromes CLL multiple myeloma, nonHodgkin lymphoma SGN-40 Seattle Genetics AML, myelodysplastic syndromesCLL multiple myeloma, non Hodgkin lymphoma SGN-75 (vorsetuzumabmafodotin) Seattle Genetics non-Hodgkin lymphoma, renal cancersibroturtumab Life Science Pharmaceuticals colorectal, head and neck,lung cancers Sym004 EMD Serono, Symphogen head and neck cancer, solidtumors tabalumab (BAFF inhibitor) Eli Lilly multiple myeloma Tarvacin ™(bavituximab) Peregrine Pharmaceuticals solid tumors TF2 Immunomedicsdiagnosis of colorectal cancer TG-1101 (ublituximab) TG TherapeuticsCLL, non-Hodgkin lymphoma tigatuzumab Daiichi Sankyo breast cancer,liver cancer, ovarian cancer, pancreatic cancer TNX-650 Tanox refractoryHodgkin lymphoma trastuzumab emtansine (T-DM1) Genentech, RocheHER2-positive metastatic breast cancer, early HER2-positive breastcancer, advanced HER2-positive gastric cancer TRC105 TRACONPharmaceuticals bladder cancer, liver cancer, ovarian cancer, prostatecancer, solid tumors tremelimumab (anti-CTLA4 mAb) AstraZeneca,MedImmune solid tumors, metastatic melanoma, prostate cancer tumorimmunotherapy mAb Genentech solid tumors U3-1565 Daiichi Sankyo solidtumors urelumab (anti-CD137) Bristol-Myers Squibb cancer VAY736MorphoSys, Novartis CLL Pharmaceuticals VB4-845 Viventia Biotechnologiesbladder cancer Vectibix ® (panitumumab) Amgen colorectal cancer VEGFR3mAb (IMC-3C5) Eli Lilly, ImClone Systems cancer veltuzumab (IMMU-106)Immunomedics CLL, non-Hodgkin lymphoma VGX-100 Circadian Technologiessolid tumors volociximab AbbVie NSCLC VX15 Vaccinex solid tumors Xgeva ®(denosumab) Amgen delay or prevention of bone, metastases in prostatecancer or breast cancer, giant cell tumor of the bone XmAb ® (high ADCCmAb) Boehringer Ingelheim cancer Pharmaceuticals, Xencor XmAb ® 2513(anti-CD30 mAb) Xencor Hodgkin disease, T-cell lymphoma XmAb ® 5574(anti-CD19 mAb) MorphoSys, Xencor CLL Y-90 hPAM 4 (IMMU-107)Immunomedics pancreatic cancer Yervoy ™ (ipilimumab) Bristol-MyersSquibb adjuvant melanoma, NSCLC, prostate cancer, SCLC, gastric cancer,ovarian cancer, leukemia, lymphoma, renal cell cancer zanolimumabEmergent BioSolutions peripheral T-cell lymphoma Zevalin ® (ibritumomabtiuxetan) Spectrum Pharmaceuticals diffuse large B-cell lymphoma,non-Hodgkin lymphoma Infectious diseases ABthrax ™ (raxibacumab) HumanGenome Sciences anthrax Anthim ™ (ETI-204) Elusys Therapeutics anthraxanthrax immune globulin Cangene anthrax anti-HIV-1 mAb PolymunScientific HIV infection anti-hsp90 mAb NeuTec Pharma candidiasisanti-PD-L1 Bristol-Myers Squibb hepatitis B anti-staph mAb MedImmuneprevention of staphylococcal infections Aurexis (tefibazumab) Inhibitexprevention and treatment of S. aureus bacteremia bavituximab PeregrinePharmaceuticals hepatitis C CCR5 MAb Hunan Genome Sciences HIV infectionCytolin ® (anti-CD8 mAb) CytoDyn HIV infection FGI-101-1A6 FunctionalGenetics influenza foravirumab Crucell post-exposure prevention ofrabies ibalizumab (TMB-355) TaiMed Biologics USA HIV-1 infection KB001-A(antibody-fragment product) KaloBios Pharmaceuticals, Sanofi Pseudomonasinfections in cystic Pasteur fibrosis patients, prevention ofventilator-associated pneumonia KD-247 Kaketsuken HIV-1 infectionMBL-HCV1 MassBiologics Hepatitis C MDX-066 (CDA-1) Medarex C. difficiledisease MDX-1303 Medarex, PharmAthene anthrax MEDI-557 (RSV mAb-extendedAstraZeneca, MedImmune prevention of respiratory syncytial half-life)virus (RSV) infections MK-3415A Merck Clostridium difficile infections(actoxumab/bezlotoxumab) NM01 SRD Pharmaceuticals HIV infection Numax ™(motavizumab) MedImmune RSV PRO 140 CytoDyn HIV-1 infection SAR279356(anti-PNAG mAB) Sanofi US prevention of bacterial infections Soliris ®(eculizumab) Alexion Pharmaceuticals Shiga toxin E. coli-relatedhemolytic uremic syndrome (STEC-HUS) streptococcal B vaccine conjugateNovartis Vaccines prevention of streptococcal B infections Synagis ®(palivizumab) MedImmune prevention of RSV infections Tarvacin ™Peregrine Pharmaceuticals hepatitis C TCN-032 (IgG mAb) TheracloneSciences influenza A virus infections TCN-202 Theraclone Sciences CMVinfections Thravixa ™ (fully human anthrax mAb) Emergent Bio Solutionspost-exposure treatment of anthrax TNX-355 Tanox HIV infection UB-421United Biomedical HIV-1 infection XOMA 3AB XOMA, National Institute ofbotulism Allergy and Infectious Diseases XTL 6865 XTL Biopharmaceuticalshepatitis C Blood disorders afelimomab Abbot Laboratories sepsis, septicshock Benlysta ® (belimumab) GlaxoSmithKline vasculitis BI-655075Boehringer Ingelheim blood coagulation disorders Pharmaceuticalseculizumab Alexion Pharmaceuticals paroxysmal nocturnal hemoglobinureaferroportin mAb Eli Lilly anemia hepcidin mAb Eli Lilly anemia ReoPro ®(abciximab) Eli Lilly adjunct to percutaneous coronary intervention forthe prevention of cardiac ischemic complications SelG1 SelexysPharmaceuticals sickle cell anemia urtoxazumab Teijin Pharma hemolyticuremic Cardiovascular disease AMG 145 Amgen Hypercholesterolemia,hyperlipoproteinemia type IIa anti-fibrin mAb (3B6/22 Tc-99m) Agenixdiagnosis of deep vein thrombosis, diagnosis of pulmonary embolismanti-oxLDL (BI-204/RG7418) BioInvent International, Genentechatherosclerosis anti-PCSK9 mAb (RG7652) Genentech cardiovascular diseaseGSK249320 GlaxoSmithKline stroke IL-1β antibody Eli Lilly cardiovasculardisease Ilaris ® (canakinumab) Novartis Pharmaceuticals secondaryprevention of cardiovascular events inclacumab (RG1512) Roche peripheralvascular disease MABp1 XBiotech vascular restinosis MLN 1202 MillenniumPharmaceuticals atherosclerosis pexelizumab Alexion Pharmaceuticals,acute myocardial infarction, Procter & Gamble Pharmaceuticalscardiopulmonary bypass PF-04950615 (RN316) Pfizer hypercholesterolemiaSAR236553/REGN727 Regeneron Pharmaceuticals, Sanofi hypercholesterolemia(anti-PCSK-9 mAb) US Diabetes and Related Conditions anti-CD3 mAbMacroGenics type 1 diabetes gevokizumab (IL-1B inhibitor mAb) XOMA type1 diabetes, type 2 diabetes GSK1070806 (IL-18 mAb) GlaxoSmithKline type2 diabetes Ilaris ® (canakinumab) Novartis Pharmaceuticals type 1diabetes, type 2 diabetes MABp1 XBiotech type 2 diabetes OKT3-gamma-1Johnson & Johnson type 1 diabetes teplizumab MacroGenics type 1 diabetesTRX 4 (anti-CD3) TolerRx type 1 diabetes Eye Conditions anti-factor D(RG7417) Genentech geographic atrophy associated with age-relatedmacular degeneration anti-LINGO (BI1B033) Biogen Idec optic neuritisgevokizumab (IL-1B inhibitor mAb) XOMA intermediate or posterior uveitisGSK933776A (anti-B amyloid mAb) GlaxoSmithKline age-related maculardegeneration Humira ® (adalimumab) AbbVie uveitis iSONEP ™(sonepcizumab) Lpath wet age-related macular degeneration Lucentis ®(ranibizumab) Genentech, Roche age-related macular degenerationPF-04382923 (RN6G) Pfizer age-related macular degeneration secukinumab(AIN457) Alcon Labs, Novartis uveitis Pharmaceuticals Soliris ®(eculizumab) Alexion Pharmaceuticals severe or refractory neuromyelitisoptica Genetic Disorders KRN-23 Kyowa Hakko Kirin Pharma X-linkeddominant hypophosphatemic rickets Soliris ® (eculizumab) AlexionPharmaceuticals paroxysmal nocturnal hemoglobinuria (PNH) NeurologicalDisorders AAB-002 Janssen Alzheimer Alzheimer's disease Immunotherapy,Pfizer AAB-003/PF-05236812 Janssen Alzheimer Alzheimer's diseaseImmunotherapy, Pfizer ABT-110 AbbVie chronic pain ALD403 AlderBiopharmaceuticals prevention of migraine ATI355 (anti-Nogo-A mAb)Novartis Pharmaceuticals spinal cord injury BAN2401 (amyloidbeta-protein inhibitor) BioArctic Neuroscience, Eisai Alzheimer'sdisease bapineuzumab Janssen Alzheimer Alzheimer's diseaseImmunotherapy, Pfizer crenezumab (anti-Abeta) Genentech Alzheimer'sdisease fulranumab Janssen Research & Development cancer pain GSK1223249(NOGO-A mAb) GlaxoSmithKline amyotrophic lateral sclerosis (ALS)GSK933776A (anti-B amyloid mAb) GlaxoSmithKline Alzheimer's diseaseLY2951742 (CGRP peptide) Arteaus Therapeutics, Eli Lilly migraineprevention MEDI-5117 (anti-IL-6 mAb) AstraZeneca, MedImmuneosteoarthritis pain RG1450 (gantenerumab) Roche prodromal Alzheimer'sdisease RN-307 (anti-CGRP mAb) Labrys Biologics migraine RN624 RinatNeuroscience osteoarthritis pain RN1219 Rinat Neuroscience Alzheimer'sdisease SAR228810 (anti-protofibrillar AB mAb) Sanofi US Alzheimer'sdisease solanezumab (LY2062430) Eli Lilly Alzheimer's disease tanezumabPfizer chronic pain Respiratory Disorders ABN 912 NovartisPharmaceuticals asthma, chronic obstructive pulmonary disorders (COPD)ABX-IL8 Amgen COPD ALT-836 Altor BioScience, Genentech acute lunginjury, adult respiratory distress syndrome AMG 157/MEDI-9929 Amgen,AstraZeneca asthma AMG 317 Amgen asthma AMG 761 Amgen asthma AMG 827(brodalumab) Amgen, AstraZeneca asthma benralizumab AstraZeneca,MedImmune asthma, chronic obstructive pulmonary disease (COPD)Bosatria ™ (mepolizumab) GlaxoSmithKline asthma carlumab Janssen Biotechpulmonary fibrosis CNTO-3157 Janssen Biotech asthma CNTO-5825 JanssenBiotech allergic asthma daclizumab (anti-CD25 MAb) Protein Design Labs,Roche asthma FG-3019 FibroGen idiopathic pulmonary fibrosis GS-6624(simtuzumab) Gilead Sciences idiopathic pulmonary fibrosis KB003KaloBios Pharmaceuticals severe asthma MEDI-528 (anti-TL-9 mAb)MedImmune asthma MEDI-4212 (anti-IgE mAb) AstraZeneca, MedImmune asthmaMEDI-7814 (anti-C5/C5a mAb) AstraZeneca, MedImmune COPD MEDI-8968(anti-IL-1R mAb) AstraZeneca, MedImmune COPD mepolizumab (anti-TL5 mAb)GlaxoSmithKline asthma and nasal polyposis QAX576 NovartisPharmaceuticals asthma, idiopathic pulmonary fibrosis QBX258 NovartisPharmaceuticals asthma QGE031 Novartis Pharmaceuticals allergic asthmaquilizumab (anti-M1 prime mAb) Genentech allergic asthma, allergicrhinitis reslizumab Cephalon asthma, eosinophilic esophagitis RG3637(lebrikizumab) Genentech, Roche severe asthma SAR156597 (bispecificSanofi US idiopathic pulmonary fibrosis interleukin-4/interleukin-13mAb) SAR231893 (anti-IL4 mAb) Regeneron Pharmaceuticals, Sanofi asthmaUS STX-100 Biogen Idec idiopathic pulmonary fibrosis TNX-832 Tanoxrespiratory diseases tralokinumab AstraZeneca, MedImmune asthma Xolair ®(omalizumab) Genentech, Novartis pediatric asthma Pharmaceuticals SkinDiseases AbGn-168H AbGenomics International plaque psoriasis AMG 827(brodalumab) Amgen, AstraZeneca psoriasis BT-061 AbbVie, Biotest plaquepsoriasis CNTO-1959 Janssen Biotech plaque psoriasis gevokizumab (IL-1Binhibitor mAb) XOMA acne vulgaris Humira ® (adalimumab) AbbViehidradenitis suppurativa ixekizumab (IL-17 antibody) Eli Lilly psoriasisMABp1 XBiotech acne, psoriasis MK-3222 (tildrakizumab) Merck plaquepsoriasis QGE031 Novartis Pharmaceuticals atopic dermatitis REGN846Regeneron Pharmaceuticals atopic dermatitis SAR231893 (anti-IL4 mAb)Regeneron Pharmaceuticals, Sanofi atopic dermatitis US secukinumab(AIN457) Novartis Pharmaceuticals plaque psoriasis Xolair ® (omalizumab)Genentech, Novartis chronic idiopathic urticaria PharmaceuticalsTransplantation ASKP-1240 Astellas Pharma US, Kyowa Hakko prevention oforgan transplant Kirin Pharma rejection Benlysta ® (belimumab)GlaxoSmithKline immunosuppression ORTHOCLONE OKT ® 3 Ortho Biotech acutekidney transplant rejection, (muromomab-CD3) reversal of heart and livertransplant rejection OKT3-gamma-1 Protein Design Labs, Johnson & renaltransplant rejection Johnson Simulect ® (basiliximab) NovartisPharmaceuticals prevention of renal transplant rejection Soliris ®(eculizumab) Alexion Pharmaceuticals presensitized kidney transplant(acute humoral rejection) TOL101 Tolera Therapeutics prevention oftransplant rejection Zenapax ® (daclizumab) Roche prophylaxis of acutekidney transplant rejection Other anti-IL31 Bristol-Myers Squibbimmunology anti-TWEAK (BIIB 023) Biogen Idec lupus nephritis BAX-69Baxter International lupus nephritis CNTO-5 Janssen Biotech, MorphoSysinflammation CNTO-136 (sirukumab) Janssen Biotech lupus nephritis CR0002 CuraGen kidney inflammation FB 301 CytovanceBiologics, Fountainhypersensitivity (IgE-mediated Biopharma allergic diseases) FG-3019FibroGen liver fibrosis due to chronic hepatitis B infectionfresolimumab (TGFβ antagonist) Genzyme fibrosis GS-6624 (simtuzumab)Gilead Sciences liver fibrosis, myelofibrosis GSK1070806(anti-interleukin 18 mAb) GlaxoSmithKline metabolic disorders Humira ®(adalimumab) AbbVie interstitial cystitis LY2382770 (TGF-β antibody) EliLilly diabetic nephropathy mAb Genentech metabolic disorders mepolizumab(anti-IL5 mAb) GlaxoSmithKline hypereosinophilic syndrome, eosinophlicesophagitis Meth-mAb InterveXion Therapeutics methamfetamine abuseStelara ® (ustekinumab) Janssen Biotech primary biliary cirrhosis VAY736MorphoSys, Novartis inflammation Pharmaceuticals Xolair ® (omalizumab)Genentech, Tanox peanut allergy

Non-limiting examples of protein-based or polypeptide-based biologicsinclude cytokines (e.g., interleukins), chemokines, growth factors,blood-production stimulating proteins (e.g., erythropoietin), hormones(e.g., Elonva® (follicle stimulating hormone), growth hormone), enzymes(e.g., Pulmozyme® (dornase alfa)), clotting factors, insulin, albumin,fragments thereof, conservatively modified variants thereof, analogsthereof, and combinations thereof.

Examples of cytokines include, but are not limited to, TNFα, TNF-relatedweak inducer of apoptosis (TWEAK), osteoprotegerin (OPG), IFN-α, IFN-β,IFN-γ, interleukins (e.g., IL-1α, IL-1β, IL-1 receptor antagonist(IL-1ra), IL-2, IL-4, IL-5, IL-6, soluble IL-6 receptor (sIL-6R), IL-7,IL-8, IL-9, IL-10, IL-12, IL-13, IL-15, IL-17, IL-23, and IL-27),adipocytokines (e.g., leptin, adiponectin, resistin, active or totalplasminogen activator inhibitor-1 (PAI-1), visfatin, and retinol bindingprotein 4 (RBP4)), and combinations thereof. In particular embodiments,the interleukin comprises IL-2 such as Proleukin® (aldesleukin;recombinant IL-2).

Examples of chemokines include, but are not limited to, CXCL1/GRO1/GROα,CXCL2/GRO2, CXCL3/GRO3, CXCL4/PF-4, CXCL5/ENA-78, CXCL6/GCP-2,CXCL7/NAP-2, CXCL9/MIG, CXCL10/IP-10, CXCL11/I-TAC, CXCL12/SDF-1,CXCL13/BCA-1, CXCL14/BRAK, CXCL15, CXCL16, CXCL17/DMC, CCL1, CCL2/MCP-1,CCL3/MIP-1α, CCL4/MIP-1β, CCL5/RANTES, CCL6/C10, CCL7/MCP-3, CCL8/MCP-2,CCL9/CCL10, CCL11/Eotaxin, CCL12/MCP-5, CCL13/MCP-4, CCL14/HCC-1,CCL15/MIP-5, CCL16/LEC, CCL17/TARC, CCL18/MIP-4, CCL19/MIP-3β,CCL20/MIP-3α, CCL21/SLC, CCL22/MDC, CCL23/MPIF1, CCL24/Eotaxin-2,CCL25/TECK, CCL26/Eotaxin-3, CCL27/CTACK, CCL28/MEC, CL1, CL2, CX₃CL1,and combinations thereof.

Non-limiting examples of growth factors include epidermal growth factor(EGF), heparin-binding epidermal growth factor (HB-EGF), vascularendothelial growth factor (VEGF), pigment epithelium-derived factor(PEDF; also known as SERPINF1), amphiregulin (AREG; also known asschwannoma-derived growth factor (SDGF)), basic fibroblast growth factor(bFGF), hepatocyte growth factor (HGF), transforming growth factor-α(TGF-α), transforming growth factor-β (TGF-β1, TGF-β2, TGF-β3, etc.),endothelin-1 (ET-1), keratinocyte growth factor (KGF; also known asFGF7), bone morphogenetic proteins (e.g., BMP1-BMP15), platelet-derivedgrowth factor (PDGF), nerve growth factor (NGF), β-nerve growth factor((3-NGF), neurotrophic factors (e.g., brain-derived neurotrophic factor(BDNF), neurotrophin 3 (NT3), neurotrophin 4 (NT4), etc.), growthdifferentiation factor-9 (GDF-9), granulocyte-colony stimulating factor(G-CSF), granulocyte-macrophage colony stimulating factor (GM-CSF),myostatin (GDF-8), erythropoietin (EPO), thrombopoietin (TPO), andcombinations thereof.

Examples of receptor construct-based or fusion protein-based biologicsinclude, but are not limited to, naturally-occurring receptors linked toan immunoglobulin frame (e.g., Orencia® (abatacept; immunoglobin CTLA-4fusion protein), Amevive® (alefacept; IgG1 fusion protein), ENBREL®(etanercept; recombinant human TNF-receptor fusion protein), engineeredproteins combining two different polypeptide species (e.g., Ontak®(denileukin diftitox; engineered protein comprising interleukin-2 anddiphtheria toxin), and combinations thereof.

The present invention can therefore be used in methods for detecting andmeasuring the presence or level of a biologic in a sample from a subjectreceiving biologic therapy for one or more of the diseases or disordersreferred to herein and Table 1, including one or more of the following:

Inflammatory diseases, such as inflammatory bowel disease (IBD) (e.g.,Crohn's disease (CD) and ulcerative colitis (UC)), uveitis, sarcoidosis,Wegener's granulomatosis, and other diseases with inflammation as acentral feature;

Autoimmune diseases, such as rheumatoid arthritis (RA), multiplescleorisis (MS), systemic lupus erythematosus (SLE), ankylosingspondylitis (Bechterew's disease), lupus, psoriatic arthritis, juvenileidiopathic arthritis, psoriasis, erythematosus, and celiac disease;

Cancer, such as digestive and gastrointestinal cancers (e.g., colorectalcancer, small intestine (small bowel) cancer; gastrointestinal stromaltumors, gastrointestinal carcinoid tumors, colon cancer, rectal cancer,anal cancer, bile duct cancer, gastric (stomach) cancer; esophagealcancer; appendix cancer; and the like); gallbladder cancer; livercancer; pancreatic cancer; breast cancer; lung cancer (e.g., non-smallcell lung cancer); prostate cancer; ovarian cancer; renal cancer (e.g.,renal cell carcinoma); cancer of the central nervous system; skincancer; choriocarcinomas; head and neck cancers; hematologicalmalignancies (e.g., leukemia, lymphoma such as B-cell non-Hodgkin'slymphoma); osteogenic sarcomas (e.g., Ewing sarcoma); soft tissuesarcomas (e.g., Dermatofibrosarcoma Protuberans (DFSP),rhabdomyosarcoma); other soft tissue malignancies, and papillary thyroidcarcinomas;

Infectious diseases, such as C. difficile disease, respiratory syncytialvirus (RSV), HIV, anthrax, candidiasis, staphylococcal infections, andhepatitis C;

Blood disorders, such as sepsis, septic shock, paroxysmal nocturnalhemoglobinuria, and hemolytic uremic syndrome;

Cardiovascular disease, such as atherosclerosis, acute myocardialinfarction, cardiopulmonary bypass, and angina;

Metabolic disorders, such as diabetes, e.g., type 1 diabetes mellitusand type 2 diabetes;

Genetic disorders, such as paroxysmal nocturnal hemoglobinuria (PNH);

Neurological disorders, such as osteoarthritis pain and Alzheimer'sdisease;

Respiratory disorders, such as asthma, chronic obstructive pulmonarydisorders (COPD), nasal polyposis, and pediatric asthma;

Skin diseases, such as psoriasis, including chronic moderate to severeplaque psoriasis;

Transplant rejection, such as acute kidney transplant rejection,reversal of heart and liver transplant rejection, prevention of renaltransplant rejection, prophylaxis of acute kidney transplant rejection,and renal transplant rejection; and/or

Other disorders, such as kidney inflammation, postmenopausalosteoporosis (bone disorders), hypereosinophilic syndrome, eosinophilicesophagitis, and peanut allergy.

In particular embodiments, the subject has an inflammatory disease(e.g., inflammatory bowel disease (IBD) such as Crohn's disease (CD) orulcerative colitis (UC)) or an autoimmune disease (e.g., rheumatoidarthritis).

VIII. Examples

The following examples are offered for illustrative purposes, and arenot intended to limit the invention in any manner. Those of skill in theart will readily recognize a variety of non-critical parameters whichcan be changed or modified to yield essentially the same results.

Example 1

This example illustrates the validation of a homogeneous mobility shiftassay (HMSA) for the measurement of vedolizumab (VLM) and anti-VLMantibodies (ATV) in inflammatory bowel disease (IBD) patient serum.

Vedolizumab (VLM), an α4β7 integrin antagonist, is a therapeuticmonoclonal antibody recently approved for use in moderate to severeulcerative colitis or Crohn's disease patients that have failed todemonstrate adequate response to conventional therapies or TNF alphaantagonists. α4β7 integrin is a gut-specific heterodimeric glycoproteinthat is important for leukocyte homing to sites of inflammation withinthe intestine, via its interaction with mucosal addressin cell adhesionmolecule-1 (MadCam-1) expressed on the intestinal vascular endothelium.Availability of diagnostic tests to accurately measure VLM drug levelsand anti-VLM antibodies is necessary for the effective use of this noveltherapeutic in IBD patients. In succession with our anti-TNF alphatherapeutic drug monitoring assays, we have now developed and validatedassays to measure VLM and anti-VLM levels in patient serum.

Methods

Soluble α4β7 protein heterodimer was expressed and purified frommammalian cells (e.g., CHO cells). In particular, the integrin α4subunit was truncated after the thigh domain (α4Δ620) and integrin β7after the I-EGF 1 domain (β7Δ527) (see, FIG. 13 ). Acidic/Basicα-helical coiled coil peptides containing one disulfide-bridge formingCys residue were attached to the C-terminus of the subunits to stabilizethe heterodimer (Takagi et al., Embo J., 18:4607-4615 (2003); O'Shea etal., Curr. Biol., 3:658-667 (1993)). A hexahistidine tag was fused tothe C-terminus of the basic peptide to facilitate purification. Thisrecombinant heterodimer was used in a “competition” based homogeneousmobility shift assay (HMSA) format to measure VLM levels in sera ofpatients on VLM therapy. Patient serum was combined with α4β7 to allowtherapeutic VLM to bind with α4β7. Subsequently, fluorescently labeledVLM competed with unlabeled VLM is patient sera for binding to itstarget, α4β7 followed by separation on HPLC size exclusionchromatography. The amount of “free” VLM-alexa fluor determined VLMlevels in patient sera. For the anti-VLM assay, standard curves werecreated by incubating normal human serum containing known amounts ofrabbit anti-VLM antibodies with fluorescently labeled VLM; bound andfree VLM were then separated by SEC-HPLC. Method validation wasdetermined according to industry recommendations.

Results

Sensitivity for VLM was 0.35 μg/mL. The lower and upper limits ofquantitation (LLOQ and ULOQ) were determined to be 0.625 μg/ml and 14μg/mL, respectively. For anti-VLM, the LLOQ and ULOQ were 3.13 U/ml and150 U/ml, respectively. The standard curves generated for each assayshowed high reproducibility and sensitivity. Inter- and intra-assayprecision showed less than 10% CV and accuracy was within 20%. There wasno significant interference from lipemic, hemolyzed, or rheumatoidfactor (Rf) serum. See, FIGS. 4-10 .

Conclusions

A sensitive and specific assay has been developed and validated tomeasure VLM and anti-VLM levels in patients undergoing treatment forIBD. The assay format required a unique approach owing to the complexityof a large heterodimeric, heavily glycosylated membrane bound antigen asdrug target. Both the drug and anti-drug assays demonstrate highaccuracy and precision with high sensitivity with a high tolerance toknown interfering agents. The assays are useful for clinical monitoringand drug optimization in individual patients.

Example 2

This example illustrates the validation of a homogeneous mobility shiftassay (HMSA) and for the measurement of ustekinumab (UTK) andantibodies-to-ustekinumab (ATU) in inflammatory bowel disease (IBD)patient serum.

Ustekinumab is a therapeutic monoclonal antibody which has potentialutility in the treatment of IBD in patients that have failed to respondto conventional therapies or TNF alpha antagonists. Ustekinumab is amonoclonal antibody with specificity for interleukin 12 and interleukin23 via their common p40 subunit and blocks inflammation through thesepathways. Here we describe the analytical validation of a HPLC-basedhigh mobility shift assay to measure UTK as well asantibodies-to-ustekinumab.

Methods

Recombinant, soluble IL12p40 subunit (e.g., SEQ ID NO:7) was expressedand purified from mammalian cells. The assay takes advantage offluorescently labeled UTK competing with unlabeled UTK in patient serafor binding to IL12p40. After incubation of patient sera withrecombinant IL12p40, UTK-alexa fluor 488 was added, before runningsamples on an HPLC size exclusion column which separates “free”UTK-alexa fluor 488 from UTK-alexa fluor 488 which is bound to IL12p40.The amount of “free” UTK-alexa fluor 488 is a measure of the amount oftherapeutic UTK in patient sera. The area under the curve (AUC) of the“free” UTK-alexa fluor 488 is plotted against the log of the UTKconcentration in known standard samples and UTK concentration in patientsera are calculated by interpolation. For the ATU assay, standard curveswere created by incubating normal human serum containing known amountsof rabbit ATU with fluorescently labeled UTK; bound and free GLM werethen separated by SEC-HPLC. Method validation was determined accordingto industry recommendations.

Results

Sensitivity for UTK was 0.15 μg/ml. The upper limit of quantitation(ULOQ) was determined to be 8 μg/mL and the lower limit of quantitation(LLOQ) was determined to be 0.625 μg/ml. For ATU, the LLOQ and ULOQ were3.13 U/ml and 150 U/ml respectively. The standard curves generated foreach assay showed high reproducibility and sensitivity. Inter- andintra-assay precision showed less than 10% CV and accuracy was within20%. There was no significant interference from lipemic, hemolyzed, orrheumatoid factor (Rf) serum. See, FIGS. 11-12 .

Conclusions

This study describes the validation of a novel “competition” based assayto measure ustekinumab levels in patients undergoing treatment for IBD.The assay format required a unique approach owing to complexity ofworking with this antigen, due to its tendency to form homodimers andheterodimers in serum making usage of a conventional HMSA assaydifficult.

The competition-based HMSA assay showed high accuracy and precision withhigh sensitivity. In addition, the assay has high tolerance to knowninterfering agents. These assays are useful for clinical monitoring anddrug optimization in individual patients.

Example 3

This example illustrates an exemplary vedolizumab (VLM)competition-based assay methodology of the present invention. One ofordinary skill in the art will appreciate that the assay methodologydescribed in this example is applicable to determining the presence orlevel of ustekinumab (UTK) as well as other biologics in a sample insituations where the complexity of working with the antigen that bindsto the biologic (e.g., the antigen is a membrane-bound protein, aglycosylated protein, a multimeric protein, an insoluble protein, aprotein that is difficult to express or purify, and/or a large protein)necessitate the use of a soluble form (e.g., a soluble fragment,variant, or monomer) of the antigen.

Normal human serum (NHS) samples spiked with known amounts ofvedolizumab (VLM) are serially diluted. Two-fold serial dilutionsstarting from 80 μg/ml VLM are diluted in NHS to make 10-point curve(i.e., 80 μg/ml to 0.15625 μg/ml). NHS spiked with 12, 4, and 1 μg/mlVLM are used as positive controls. Standard serum samples, positivecontrols, and patient samples are added to a 96 well plate. Patientsamples are added undiluted or diluted 4× or 8× in NHS to increase theassay dynamic range. Soluble α4β7 antigen and assay diluent are added.The plate is placed on a shaker and allowed to incubate at roomtemperature for 1 hour. After 1 hour, labeled VLM (e.g., VLM-AlexaFluor® 488) is added. The plate is again placed on a shaker for a 1 hourincubation. Samples are filtered using a 0.2 μm filter plate. Samplesare loaded onto an HPLC autosampler and run sequentially through a sizeexclusion chromatography column (e.g., a Phenomenex BioSep-SEC-s3000column) which separates free labeled VLM (e.g., VLM-Alexa Fluor® 488)from labeled VLM bound to the soluble α4β7 antigen.

Software written in R-programming language is used to identify the peakrepresenting free labeled VLM (e.g., VLM-Alexa Fluor® 488) and todetermine the area of the peak. The area of this peak gets larger whenthere is VLM in the patient's sera. By comparing the size of this peakto the standard curve, one can interpolate the patient's VLM levels.

Prism (e.g., GraphPad Prism 6) is used to generate a standard curve byplotting the area of free labeled VLM (e.g., VLM-Alexa Fluor® 488) as afunction of serum VLM levels. By comparing the size of this peak to thestandard curve, one can interpolate the patient's VLM drugconcentration.

The assay described in this example is premised on the competitionbetween the VLM in a sample from a patient receiving VLM therapy and thelabeled VLM added to the sample reaction for binding to the soluble α4β7antigen. The relative ratios of labeled and unlabeled VLM determines howmuch α4β7 antigen is bound to each and determines the free labeled VLM(e.g., VLM-Alexa Fluor® 488) peak area. The more drug present in thepatient sample, the more the labeled VLM remains free as opposed tobound to the α4β7 antigen.

Example 4

This example illustrates the validation of a homogeneous mobility shiftassay (HMSA) for the measurement of vedolizumab (VLM) and anti-VLMantibodies in inflammatory bowel disease (IBD) patient serum.

Background and Aims

Vedolizumab, an α4β7 integrin antagonist, is a therapeutic monoclonalantibody recently approved for use in moderate to severe ulcerativecolitis and Crohn's disease patients that have failed to demonstrateadequate response to conventional therapies or TNFα antagonists.Availability of diagnostic tests to accurately measure serum VLM andanti-VLM (ATV) levels is necessary for the effective use of this noveltherapeutic in IBD patients. Here we describe the analytical validationof the HMSA developed to measure VDM and ATV levels in patient serum aswell as its clinical utility.

Methods

Soluble α4β7 heterodimer (e.g., α4Δ620/β7Δ527 heterodimer; see, FIG. 13) was expressed and purified in mammalian cells. This recombinantheterodimer was used in a “competition” based HMSA format to measureserum VLM levels in patients on VLM therapy. Patient serum was combinedwith α4β7 to allow therapeutic VLM to bind with α4β7. Subsequently,fluorescently labeled VLM competed with unlabeled VLM in patient serafor binding to its target, α4β7, followed by separation on HPLC sizeexclusion chromatography (see, FIG. 1 ). For the anti-VLM assay,standard curves were created by incubating normal human serum containingknown amounts of rabbit anti-VLM antibodies with fluorescently labeledVLM; bound and free VLM were then separated by SEC-HPLC. Validation wasperformed according to industry recommendations (Shankar, G., et al.2008).

Results

VLM and ATV assays show high intra-assay precision and accuracy.Intra-assay precision is less than 10% and intra-assay accuracy is lessthan 15% error. Run to run, instrument to instrument, and analyst toanalyst variability are less than 15% CV and less than 20% error inalmost all cases. (Table 2). Sensitivity for VLM was 0.348 μg/mL with adynamic range of 0.625-14 μg/mL (Table 3). The limit of detection forthe ATV assay is <1.56 U/mL. A precise value could not be determined asit is too low to interpolate our curve. The dynamic range for ATV was3.13-150 U/mL in undiluted serum (Table 3). Normal human serum spikedwith VLM or ATV showed good linearity and recovery across serialdilutions (FIGS. 14A and 14B). ATV shows high drug tolerance at levelsof 20 μg/mL of VLM (Table 4). Common interfering agents in patient serumwere tested and did not interfere at levels seen in IBD patients (FIGS.15A, 15B and 15C).

TABLE 2 Validation data for accuracy and precision of the assays.Accuracy and Precision of the VLM-HMSA Inter-Assay Precision Intra-AssayPrecision Instrument Run to Run Analyst to Analyst to Instrument (n =10) (n = 10) (n = 5) (n = 10) Hgh Med Low High Med Low High Med Low HighMed Low Expected 12 4 1 12 4 1 12 4 1 12 4 1 (μ/mL) Measured 10.34 4.360.89 11.22 4.16 1.13 10.51 4.19 1.05 12.30 4.18 1.29 (Mean, U/mL) SD0.56 0.21 0.10 1.11 0.17 0.18 0.47 0.33 0.16 0.86 0.19 0.08 CV % 5.454.82 11.64 9.87 4.07 14.53 4.46 7.97 14.91 6.97 4.44 6.07 Accuracy 13.839.07 11.00 6.48 3.91 12.72 12.44 4.76 5.30 2.46 4.44 29.04 (% Error)Accuracy and Precision of the ATV-HMSA Inter-Assay Precision Intra-AssayPrecision Instrument Run to Run Analyst to Analyst to Instrument (n =10) (n = 10) (n = 10) (n = 10) Hgh Med Low High Med Low High Med LowHigh Med Low Expected 50 25 12.5 50 25 12.5 50 25 12.5 50 25 12.5 (U/mL)Measured 47.31 23.32 11.72 51.53 25.01 13.54 51.52 25.56 13.51 47.3123.34 11.75 (Mean, U/mL) SD 2.82 1.51 0.79 5.00 3.39 1.76 5.00 2.43 1.862.73 1.46 0.78 CV % 5.96 6.46 6.75 9.71 13.56 13.00 9.71 9.52 13.78 5.776.25 6.62 Accuracy 5.37 6.71 6.27 7.93 0.04 8.32 3.04 2.25 8.06 5.386.65 5.96 (% Error)

TABLE 3 Limits of quantitation for each assay. Lower Upper Limit ofLimit of Limit of Limit of Assay Blank Detection QuantitationQuantitation VLM-HMSA n = 30 n = 30 n = 36 n = 36 0.054 μg/mL 0.348μg/mL 0.625 μg/mL 14 μg/mL ATV-HMSA n = 25 n = 25 n = 36 n = 36 <1.56U/mL <1.56 U/mL 3.13 U/mL 150 U/mL

TABLE 4 Drug interference in the anti-VLM assay. Vedo [μg/mL] Total ATV[U/mL] 20 51.6 0 49.2 20 26.4 0 24.8 20 13 0 14Conclusions

A sensitive and specific assay has been developed and validated tomeasure VLM and anti-VLM levels in patients undergoing treatment forIBD. The assay format required a unique approach owing to the complexityof a large heterodimeric, heavily glycosylated membrane protein as drugtarget. Both the drug and anti-drug assays demonstrate high accuracy andprecision with tolerance to known interfering agents. The development ofVLM and anti-VLM assays is useful for clinical monitoring and drugoptimization in individual patients.

Example 5

This example illustrates the validation of a homogeneous mobility shiftassay (HMSA) for the measurement of ustekinumab (UTK) andantibodies-to-ustekinumab (ATU) in inflammatory bowel disease (IBD)patient serum.

Background and Aims

Ustekinumab is a therapeutic monoclonal antibody which has potentialutility in the treatment IBD patients that have failed to respond toconventional therapies or TNFα antagonists. Ustekinumab is specific forIL-12 and IL-23 via their common p40 subunit and blocks inflammationthrough these pathways. Availability of diagnostic tests to accuratelymeasure serum UST and anti-UST (ATU) levels is necessary for theeffective use of this novel therapeutic in IBD patients. Here wedescribe the analytical validation of a “competition” based HMSAdeveloped to measure UTK levels as well as conventional HMSA to measureATU levels in patient serum.

Methods

Recombinant, soluble IL12p40 (e.g., SEQ ID NO:7) was expressed andpurified from mammalian cells. Recombinant IL12p40 was used in a“competition” based HMSA format to measure serum UTK levels in patientson UTK therapy. Patient serum was combined with rIL12p40 to allowtherapeutic UTK to bind with rIL12p40. Subsequently, fluorescentlylabeled UTK competed with unlabeled UTK in patient sera for binding toits target, rIL12p40, followed by separation on HPLC size exclusionchromatography (see, FIG. 16 ). For the anti-UTK assay, standard curveswere created by incubating normal human serum containing known amountsof rabbit anti-UTK antibodies with fluorescently labeled UTK; bound andfree UTK were then separated by SEC-HPLC.

Results

UTK and ATU assays show high intra-assay precision and accuracy.Intra-assay precision is less than 10% and intra-assay accuracy is lessthan 15% error. Run to run, instrument to instrument, and analyst toanalyst variability are less than 15% CV and less than 20% error. (Table5). Sensitivity for UTK is 0.224 μg/mL with a dynamic range of 0.625-10μg/mL (Table 6). The limit of detection for the ATU assay is <1.56 U/mL.A precise value could not be determined as it is too low to interpolatefrom the standard curve. The dynamic range for ATU is 3.13-150 U/mL inundiluted serum (Table 6). Normal human serum spiked with UTK or ATUshowed good linearity and recovery across serial dilutions within theassay's dynamic range (FIGS. 17A and 17B). ATU shows high drugtolerance. Levels of 20 μg/mL of UTK do not significantly interfere withATU detection (Table 7). Common interfering agents in patient serum weretested and did not interfere at levels seen in IBD patients. Only highlyhemolyzed serum may potentially interfere but not at levels normallyseen in patient sera (FIGS. 18A, 18B and 18C).

TABLE 5 Validation data for precision and accuracy of the assays.Accuracy and Precision of the UTK-HMSA Inter-Assay Precision Intra-AssayPrecision Instrument Run to Run Analyst to Analyst to Instrument (n = 5)(n = 5) (n = 5) (n = 5) Hgh Med Low High Med Low High Med Low High MedLow Expected 10 5 2.5 10 5 2.5 10 5 2.5 10 5 2.5 (μg/mL) Measured 8.894.52 2.40 10.59 5.03 2.59 10.09 4.93 2.66 10.29 5.26 2.89 (Mean, μg/mL)SD 0.62 0.08 0.05 0.97 0.29 0.13 0.52 0.27 0.18 0.49 0.29 0.09 CV % 6.961.76 2.16 9.18 5.67 5.06 5.18 5.39 6.95 4.79 5.44 3.15 Accuracy 11.149.55 4.03 5.88 0.69 3.71 0.94 1.42 6.23 2.87 5.28 15.43 (% Error)Accuracy and Precision of the ATU-HMSA Inter-Assay Precision Intra-AssayPrecision Instrument Run to Run Analyst to Analyst to Instrument (n = 5)(n5) (n = 5) (n = 5) Hgh Med Low High Med Low High Med Low High Med LowExpected 50 20 10 50 20 10 50 20 10 50 20 10 (U/mL) Measured 49.61 21.089.47 50.63 21.51 9.20 51.24 21.48 9.19 49.61 20.39 8.78 (Mean, U/mL) SD0.33 0.83 0.78 1.16 0.73 0.60 1.80 0.73 0.61 1.85 0.69 0.20 CV % 0.673.95 8.27 2.30 3.39 6.52 3.51 3.39 6.60 3.74 3.37 2.30 Accuracy 0.795.42 5.30 1.25 7.54 7.96 2.47 7.41 8.11 0.79 1.97 12.23 (% Error)

TABLE 6 Limits of quantitation for each assay. Limits of QuantitationLower Upper Limit of Limit of Limit of Limit of Assay Blank DetectionQuantitation Quantitation UTK-HMSA n = 30 n = 30 n = 36 n = 36 0.077μg/mL 0.224 μg/mL 0.625 μg/mL 10 μg/mL ATU-HMSA n = 30 n = 30 n = 30 n =30 Too low to <1.56 U/mL 3.13 U/mL 150 U/mL interpolate

TABLE 7 Drug interference in the anti-UTK assay. UTK [μg/mL] Total ATU[U/mL] 20 58.8 0 51.7 20 16.7 0 22.1 20 5.6 0 9.2Conclusions

HMSA for UTK and ATU showed high accuracy and precision across a widedynamic range. The HMSA platform allowed detection of UTK and ATU evenin the presence of interfering agents which are known to limit theutility of ELISA/ECLIA methods. The development of a new “competition”based HMSA platform allows for the measurement of therapeutic druglevels when a conventional HMSA is not feasible.

Example 6

This example illustrates experiments performed to improve the dynamicrange of the homogeneous mobility shift assay (HMSA) for the measurementof vedolizumab (VDZ).

In an effort to improve the assay's dynamic range, the assay wasmodified by increasing the amount of VDZ-Alexa488 used in the assay1.6-fold. Increasing the amount of labeled VDZ and proportionatelyincreasing the amount of α4β7 antigen (e.g., α4Δ620/β7Δ527 heterodimer;see, FIG. 13 ) increased the dynamic range of the assay. In addition,changing the amount of α4β7 relative to labeled VDZ affected the lowerlimit of quantification. Excess antigen relative to labeled VDZ made theassay relatively insensitive to drug in patient sera and raised thelower limit of quantification. Conversely, too little antigen relativeto labeled VDZ had the effect of lowering the upper limit ofquantification. Increasing the amount of labeled VDZ from 75 ng/well to120 ng/well (1.6-fold) and titrating the antigen such that the presenceof antigen binds up 75-80% of the labeled VDZ provided the bestcompromise between the low-end sensitivity needed as well as an improveddynamic range that would enable the measurement of drug in patient serawithout requiring dilutions in most cases.

In addition, the data is plotted such that the area of the VDZ-Alexa488peak (without dividing by the Blocked-Alexa 488 control peak area) isplotted against the log of the VDZ concentration.

1. Assay Limits

Limit of Blank

The Limit of Blank (LOB) was determined from 30 replicates of thestandard curve blank. The standard curve blank (negative control) in allassays consisted of 4% normal human serum+40 ng VDZ-Alexa488+165 ng α4β7per 100 μL injection. The average (mean)+1.645SD of the VDZ-Alexa488peak area was calculated and then used for calculation of the LOD.

TABLE 8 Assay Limit of Blank (LOB). N 30 Mean (VDZ-Alexa488 peak area)1.91 SD (VDZ-Alexa488 peak area) 0.09 The average (mean) + 1.645 SD 2.06Interpolated LOB 0.156/ml* *The average (mean) + 1.645 SD was just belowthe lowest point of the curve and therefore the lowest point on thecurve was taken for the LOB.Limit of Detection

The Limit of Detection (LOD) was determined by utilizing the measuredLOB and replicates of serum containing VDZ at a low concentration whichis approaching the LOB. Standard 10 was chosen because it is the lowestpoint on the curve and nearest the LOB. The LOD was calculated using theequation: LOD=LOB+1.645(SD_(low concentration sample)) (Armbruster etal., 2008). The value was then interpolated from the averaged standardcurve of the experiments used in the calculation to yield theconcentration in μg/mL.

TABLE 9 Assay Limit of Detection. N 30 Mean (VDZ-Alexa488 peak area)1.91 SD (VDZ-Alexa488 peak area) 0.061 1.645*SD 0.100 Interpolated(1.645*SD) Too low to interpolate LOD = The average (mean) + 3*SD 0.457μg/mLLimit of Quantitation

The Lower Limit of Quantitation (LLOQ) was determined by analyzinginterpolated concentrations of 30 replicates of a low concentration VDZpositive sample. In this case, standard 8 (effective serum concentrationof 0.625 μg/mL) was chosen. The upper limit of quantitation (ULOQ) wasdetermined by analyzing 30 replicates of a high concentration VDZpositive sample (effective serum concentration equal to 14 μg/mL). LLOQwas defined as the concentration that results in a CV≤20% with Error≤25%and thus measures the assay's precision and accuracy at a low analyteconcentration. The ULOQ was also qualified by CV≤20% with Error≤25%.

TABLE 10 LLOQ and ULOQ. LLOQ ULOQ N 30 30 Expected (μg/mL) 1 25 Mean(μg/mL) 1.05 20.95 SD (μg/mL) 0.12 1.44 CV (%) 11.39 6.86 Error (%) 5.13−16.19These criteria resulted in the following values for the Assay Limits:

TABLE 11 Assays Limits of Quantitation. LOD 0.457 μg/mL LLOQ    1 μg/mLULOQ   25 μg/mL2. InterferenceAntibody to Vedolizumab (ATV) Interference

In this experiment, 2.5, 5, 10 and 20 μg/mL VDZ was added to eithernormal human serum or various concentrations of rabbit ATV positiveserum. These samples were then analyzed using the assay and the %recovery calculated.

TABLE 12 ATV Interference. Measured VDZ VDZ (μg/mL) spike Control %Recovery (μg/mL) (No ATV) 0 U/mL 3.13 U/mL 6.25 U/mL 12.5 U/mL 25 U/mL50 U/mL 2.5 2.23 100 90 82 62 0 0 5 4.47 100 93 88 77 60 22 10 9.15 10091 85 77 71 55 20 17.53 100 87 81 73 69 59

The assay tolerance to ATV is up to 6.25 U/ml in this experiment. TheATV interference is expected as neutralizing ATV will compete with α4β7for binding to patient VDZ. Only VDZ bound to non-neutralizing ATV isexpected to be detected.

Integrin α4β7 Substrate Interference

To test the interference of α4β7, titrations were performed in the rangeof 1 to 1000 ng/mL. VDZ concentrations were plotted on the intercept ofthe X-axis correspond to the zero concentration of each interferingagent (FIG. 19 ).

TABLE 13 α4β7 Interference (100 ng/mL). VDZ Positive High Control MediumControl Low Control Control (12 μg/mL) (4 μg/mL) (1 μg/mL) Mean (μg/mL)12.57 3.77 1.22 SD (μg/mL) 0.23 0.01 0.04 CV (%) 1.8 0.3 3.5 Recovery(%) 109.6 108.1 106.7

There was no significant interference from levels of α4β7 far exceedinglevels one would expect to see in sera from patients being treated withVDZ.

3. Antigen Stability

The stability of α4β7 antigen was assessed through storage at 4 degrees(4° C.) for 1 week. After 1 week, the α4β7 was removed from 4° C.storage and analyzed against a fresh aliquot stored at −70° C. The datafrom the 4° C. storage samples was then compared to that obtained beforestorage and the percent error calculated. The aliquots were deemedstable at 4° C. if the error was within 25%.

TABLE 14 Accelerated Stability. Time Point Week 0 Week 1 VDZ Pos. CtrlHigh Med Low High Med Low 4° C. Mean (μg/mL) 10.00 3.15 0.88 11.06 4.421.12 SD (μg/mL) 0.21 0.45 0.06 0.81 0.21 0.06 CV (%) 2.11 14.24 6.657.32 4.81 5.21 Error (%) −16.64 −21.35 −12.34 −7.81 10.50 12.05

Accelerated stability of α4β7. Antigen stored at −70° C. was used in theassay to test VDZ positive controls. Controls came out withinspecifications (Error≤25% and CV≤25%). Antigen stored at 4° C. was usedin the assay to test VDZ positive controls. These controls also came outwithin specifications. In addition, there was no obvious loss of antigenpotency as a result of being stored at 4° C. versus −70° C.

4. Additional Dynamic Range Experiments

Three standard curves were generated using a 1× amount of labeled VDZ(e.g., 75 ng/well of VDZ-Alexa488), as well as 2× and 4× amounts. FIG.20 shows that proportionately increasing the concentrations of bothVDZ-Alexa488 and integrin α4β7 used in the assay increases the assay'sdynamic range. It also increases anti-drug antibody tolerance. A maximumLLOQ of 1 μg/mL was the criteria for this assay. In particular,increasing the amount of labeled VDZ and α4β7 by 1.6-fold enabled amaximum LLOQ of 1 μg/mL while providing an improved top-end range of 25μg/mL (see, Table 11).

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, one of skill in the art will appreciate that certainchanges and modifications may be practiced within the scope of theappended claims. In addition, each reference provided herein isincorporated by reference in its entirety to the same extent as if eachreference was individually incorporated by reference.

INFORMAL SEQUENCE LISTING SEQ ID NO: 1 Human alpha 4 integrin fragmentMAWEARREPGPRRAAVRETVMLLLCLGVPTGRPYNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRIGKNPGQTCEQLQLGSPNGEPCGKTCLEERDNQWLGVTLSRQPGENGSIVTCGHRWKNIFYIKNENKLPTGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYTKDLIVMGAPGSSYWTGSLFVYNITTNKYKAFLDKQNQVKFGSYLGYSVGAGHFRSQHTTEVVGGAPQHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTIREEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQEDDLQGAIYIYNGRADGISSIFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAFRSDSAVLLRIRPVVIVDASLSHPESVNRIKFDCVENGWPSVCIDLTLCFSYKGKEVPGYIVLEYNMSLDVNRKAESPPREYESSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILTPIQIEAAYHLGPHVISKRSTEEFPPLQPILQQKKEKDIMKKTINFARSEQ ID NO: 2 Human beta 7 integrin fragmentMVALPMVLVLLLVLSRGESELDAKIPSTGDATEWRNPHLSMLGSCQPAPSCQKCILSHPSCAWCKQLNFTASGEAEARRCARREELLARGCPLEELEEPRGQQEVLQDQPLSQGARGEGATQLAPQRVRVILRPGEPQQLQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVIHSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLIGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQEQIGWRNVSRLLVFTSDDIFHTAGDGKLGGIFMPSDGHCHLDSNGLYSRSTEFDYPSVGQVAQALSAANIQPIFAVISAALPVYQELSKLIPKSAVGELSEDSSNVVQLIMDAYNSLSSIVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVIFWVSLQATHCLPEPHLLRLRALGESEELIVELHTLCDCNCSDIQPQAPHCSDGQGHLQCGVCSCAPGRLGRLCECSVAELSSPDLESGC SEQ ID NO: 3Human alpha 4 integrin fragment with acidic peptideMAWEARREPGPRRAAVRETVMLLLCLGVPIGRPYNVDTESALLYQGPHNTLFGYSVVLHSHGANRWLLVGAPTANWLANASVINPGAIYRCRIGKNPGQICEQLQLGSPNGEPCGKICLEERDNQWLGVILSRQPGENGSIVICGHRWKNIFYIKNENKLPIGGCYGVPPDLRTELSKRIAPCYQDYVKKFGENFASCQAGISSFYIKDLIVMGAPGSSYWIGSLEVYNITINKYKAFLDKQNQVKFGSYLGYSVGAGHERSQHTTEVVGGAPQHEQIGKAYIFSIDEKELNILHEMKGKKLGSYFGASVCAVDLNADGFSDLLVGAPMQSTIREEGRVFVYINSGSGAVMNAMETNLVGSDKYAARFGESIVNLGDIDNDGFEDVAIGAPQEDDLQGAIYIYNGRADGISSIFSQRIEGLQISKSLSMFGQSISGQIDADNNGYVDVAVGAFRSDSAVLLRIRPVVIVDASLSHPESVNRIKFDCVENGWPSVCIDLTLCFSYKGKEVPGYIVLEYNMSLDVNRKAESPPREYESSNGTSDVITGSIQVSSREANCRTHQAFMRKDVRDILTPIQIEAAYHLGPHVISKRSTEEFPPLQPILQQKKEKDIMKKTINFARTGGLAQCEKELQALEKENAQLEWELQALEKELAQ SEQ ID NO: 4Human beta 7 integrin fragment with the BASE-p1 sequence of peptideVelcro containing a Cys at the ″d″ positions of the heptad repeatpeptide with TEV cleavage site and His6 tagMVALPMVLVLLLVLSRGESELDAKIPSTGDATEWRNPHLSMLGSCQPAPSCQKCILSHPSCAWCKQLNFTASGEAEARRCARREELLARGCPLEELEEPRGQQEVLQDQPLSQGARGEGATQLAPQRVRVILRPGEPQQLQVRFLRAEGYPVDLYYLMDLSYSMKDDLERVRQLGHALLVRLQEVIHSVRIGFGSFVDKTVLPFVSTVPSKLRHPCPTRLERCQSPFSFHHVLSLIGDAQAFEREVGRQSVSGNLDSPEGGFDAILQAALCQEQIGWRNVSRLLVFTSDDIFHTAGDGKLGGIFMPSDGHCHLDSNGLYSRSTEFDYPSVGQVAQALSAANIQPIFAVISAALPVYQELSKLIPKSAVGELSEDSSNVVQLIMDAYNSLSSIVTLEHSSLPPGVHISYESQCEGPEKREGKAEDRGQCNHVRINQTVIFWVSLQATHCLPEPHLLRLRALGESEELIVELHTLCDCNCSDIQPQAPHCSDGQGHLQCGVCSCAPGRLGRLCECSVAELSSPDLESGCGGLENGYFQGGKNAQCKKKLQALKKKNAQLKWKLQALKKKLAQGGHHHHHH SEQ ID NO: 5 Human IL-12p40 wild-typeMCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLICDTPEEDGITWILDQSSEVLGSGKILTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLITISIDLIFSVKSSRGSSDPQGVICGAATLSAERVRGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYISSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLIFCVQVQGKSKREKKDRVFIDKISATVICRKNASISVRAQDRYYSSSWSEWASVPC SEQ ID NO: 6Human IL-12p40 variant (C199A, C274A)MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSAAPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFAVQVQGKSKREKKDRVFIDKISATVICRKNASISVRAQDRYYSSSWSEWASVPC SEQ ID NO: 7Human IL-12p40 variant (C199A, C274A) with hexahistidine tagMCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSAAPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFAVQVQGKSKREKKDRVFIDKISATVICRKNASISVRAQDRYYSSSWSEWASVPCHHHHHH SEQ ID NO: 8ACID peptide with cysteine residue (3) AQCEKELQALEKENAQLEWELQALEKELAQSEQ ID NO: 9BASE peptide with cysteine residue (16), TEV cleavage site (3-9), andhexahistidine tag (46-51)GGLENGYFQGGKNAQCKKKLQALKKKNAQLKWKLQALKKKLAQGGHHHHHH SEQ ID NO: 10TEV cleavage site EXXYXQ/S X is any amino acid residue SEQ ID NO: 11Human IL-12p40 variant (C199S, C274S)MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSASPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFSVQVQGKSKREKKDRVFIDKISATVICRKNASISVRAQDRYYSSSWSEWASVPC SEQ ID NO: 12Human IL-12p40 variant (C199A, C274S)MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSAAPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFSVQVQGKSKREKKDRVFIDKISATVICRKNASISVRAQDRYYSSSWSEWASVPC SEQ ID NO: 13Human IL-12p40 variant (C199S, C274A)MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSASPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFAVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSTNSETNASVPC

What is claimed is:
 1. A detection method, comprising: (a) providing asample from a subject that has been administered a first biologic,wherein the sample comprises the first biologic; (b) contacting thesample with a polypeptide, wherein the polypeptide is unlabeled,isolated, and soluble; (c) contacting the polypeptide in vitro with asecond biologic; (d) indirectly detecting binding of the polypeptide tothe first biologic in the sample by measuring a form of the secondbiologic in (c), wherein the binding of the polypeptide to the secondbiologic in the sample that is detected determines a presence or anamount of the first biologic in the sample; and (e) detecting a presenceor an amount of an autoantibody to the first biologic in the sample. 2.The method of claim 1, wherein the second biologic used to contact thepolypeptide in vitro comprises a label.
 3. The method of claim 2,wherein the label comprises a fluorophore.
 4. The method of claim 1,further comprising comparing the form of the second biologic used tocontact the polypeptide in vitro to a known amount of the secondbiologic.
 5. The method of claim 1, wherein the sample is serum.
 6. Themethod of claim 1, wherein the polypeptide comprises an antigen, whereinthe antigen comprises a soluble fragment of a cell surface molecule. 7.The method of claim 1, wherein the polypeptide comprises an antigen,wherein the antigen comprises: (i) an α4 integrin polypeptide; (ii) a β7integrin polypeptide; or (iii) an α4β7 polypeptide, wherein the α4β7polypeptide comprises the α4 integrin polypeptide and the β7 integrinpolypeptide.
 8. The method of claim 7, wherein the α4 integrinpolypeptide comprises an amino acid sequence having at least 80%identity to SEQ ID NO:1 or SEQ ID NO:3, and the β7 integrin polypeptidecomprises an amino acid sequence having at least 80% identity to SEQ IDNO: 2 or SEQ ID NO:
 4. 9. The method of claim 7, wherein the α4 integrinpolypeptide comprises an ACID peptide.
 10. The method of claim 7,wherein the β7 integrin polypeptide comprises a BASE peptide.
 11. Themethod of claim 7, wherein the α4 integrin polypeptide or the β7integrin polypeptide comprises a linker.
 12. The method of claim 7,wherein the α4 integrin polypeptide or the β7 integrin polypeptidecomprises an affinity tag.
 13. The method of claim 7, wherein the α4integrin polypeptide or the β7 integrin polypeptide comprises a proteasecleavage site.
 14. The method of claim 7, wherein the first biologic andthe second biologic are vedolizumab.
 15. The method of claim 1, whereinthe polypeptide comprises an antigen, wherein the antigen comprises ap40 subunit of IL-12 or IL-23.
 16. The method of claim 15, wherein thep40 subunit comprises an amino acid sequence having at least 80%identity to SEQ ID NO: 6, 7, 11, 12, or
 13. 17. The method of claim 15,wherein the antigen further comprises an affinity tag.
 18. The method ofclaim 15, wherein the first biologic and the second biologic areustekinumab.
 19. The method of claim 1, wherein the first biologic andthe second biologic are the same type of biologic.